Class picard.sam.DownsampleSamTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testDownsampleStrategies[0](0.3, HighAccuracy, 1) | 0.153s | passed |
| testDownsampleStrategies[10](0.5, HighAccuracy, null) | 0.098s | passed |
| testDownsampleStrategies[11](0.6, HighAccuracy, null) | 0.119s | passed |
| testDownsampleStrategies[12](0.7, HighAccuracy, null) | 0.117s | passed |
| testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null) | 0.131s | passed |
| testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null) | 0.136s | passed |
| testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null) | 0.150s | passed |
| testDownsampleStrategies[16](0.3, ConstantMemory, 1) | 0.077s | passed |
| testDownsampleStrategies[17](0.4, ConstantMemory, 1) | 0.082s | passed |
| testDownsampleStrategies[18](0.5, ConstantMemory, 1) | 0.091s | passed |
| testDownsampleStrategies[19](0.6, ConstantMemory, 1) | 0.101s | passed |
| testDownsampleStrategies[1](0.4, HighAccuracy, 1) | 0.153s | passed |
| testDownsampleStrategies[20](0.7, ConstantMemory, 1) | 0.120s | passed |
| testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1) | 0.204s | passed |
| testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1) | 0.130s | passed |
| testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1) | 0.141s | passed |
| testDownsampleStrategies[24](0.3, ConstantMemory, null) | 0.063s | passed |
| testDownsampleStrategies[25](0.4, ConstantMemory, null) | 0.076s | passed |
| testDownsampleStrategies[26](0.5, ConstantMemory, null) | 0.086s | passed |
| testDownsampleStrategies[27](0.6, ConstantMemory, null) | 0.096s | passed |
| testDownsampleStrategies[28](0.7, ConstantMemory, null) | 0.107s | passed |
| testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null) | 0.119s | passed |
| testDownsampleStrategies[2](0.5, HighAccuracy, 1) | 0.160s | passed |
| testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null) | 0.132s | passed |
| testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null) | 0.144s | passed |
| testDownsampleStrategies[32](0.3, Chained, 1) | 0.076s | passed |
| testDownsampleStrategies[33](0.4, Chained, 1) | 0.083s | passed |
| testDownsampleStrategies[34](0.5, Chained, 1) | 0.092s | passed |
| testDownsampleStrategies[35](0.6, Chained, 1) | 0.104s | passed |
| testDownsampleStrategies[36](0.7, Chained, 1) | 0.115s | passed |
| testDownsampleStrategies[37](0.7999999999999999, Chained, 1) | 0.128s | passed |
| testDownsampleStrategies[38](0.8999999999999999, Chained, 1) | 0.140s | passed |
| testDownsampleStrategies[39](0.9999999999999999, Chained, 1) | 0.147s | passed |
| testDownsampleStrategies[3](0.6, HighAccuracy, 1) | 0.126s | passed |
| testDownsampleStrategies[40](0.3, Chained, null) | 0.072s | passed |
| testDownsampleStrategies[41](0.4, Chained, null) | 0.079s | passed |
| testDownsampleStrategies[42](0.5, Chained, null) | 0.091s | passed |
| testDownsampleStrategies[43](0.6, Chained, null) | 0.102s | passed |
| testDownsampleStrategies[44](0.7, Chained, null) | 0.113s | passed |
| testDownsampleStrategies[45](0.7999999999999999, Chained, null) | 0.126s | passed |
| testDownsampleStrategies[46](0.8999999999999999, Chained, null) | 0.136s | passed |
| testDownsampleStrategies[47](0.9999999999999999, Chained, null) | 0.145s | passed |
| testDownsampleStrategies[4](0.7, HighAccuracy, 1) | 0.125s | passed |
| testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1) | 0.142s | passed |
| testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1) | 0.142s | passed |
| testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1) | 0.149s | passed |
| testDownsampleStrategies[8](0.3, HighAccuracy, null) | 0.074s | passed |
| testDownsampleStrategies[9](0.4, HighAccuracy, null) | 0.084s | passed |
| testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1]) | 0.139s | passed |
| testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1]) | 0.144s | passed |
| testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1]) | 0.140s | passed |
| testRepeatedDownsampling[12]([Chained, Chained], [1, 1]) | 0.148s | passed |
| testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1]) | 0.146s | passed |
| testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1]) | 0.151s | passed |
| testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1]) | 0.148s | passed |
| testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) | 0.214s | passed |
| testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) | 0.215s | passed |
| testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) | 0.209s | passed |
| testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) | 0.240s | passed |
| testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0]) | 0.145s | passed |
| testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) | 0.212s | passed |
| testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) | 0.212s | passed |
| testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) | 0.214s | passed |
| testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) | 0.221s | passed |
| testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) | 0.214s | passed |
| testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) | 0.215s | passed |
| testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) | 0.212s | passed |
| testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) | 0.237s | passed |
| testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) | 0.214s | passed |
| testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) | 0.217s | passed |
| testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647]) | 0.139s | passed |
| testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) | 0.218s | passed |
| testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) | 0.217s | passed |
| testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) | 0.220s | passed |
| testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) | 0.211s | passed |
| testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) | 0.217s | passed |
| testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) | 0.219s | passed |
| testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648]) | 0.138s | passed |
| testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647]) | 0.138s | passed |
| testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0]) | 0.140s | passed |
| testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1]) | 0.139s | passed |
| testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1]) | 0.156s | passed |
| testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3]) | 0.159s | passed |
| testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1]) | 0.141s | passed |
Standard output
No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found No errors found
Standard error
[Thu Apr 24 13:03:52 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17202042952114654940.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.3 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:52 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:52 DownsampleSam Kept 6000 out of 20000 reads (30.00%). [Thu Apr 24 13:03:52 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:52 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17901416034166692454.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.4 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:52 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:52 DownsampleSam Kept 8000 out of 20000 reads (40.00%). [Thu Apr 24 13:03:52 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:52 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1905594234894896690.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:52 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:52 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:03:52 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:52 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11857424218618956765.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.6 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:52 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:52 DownsampleSam Kept 12000 out of 20000 reads (60.00%). [Thu Apr 24 13:03:52 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:52 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13931301301271820789.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.7 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 14000 out of 20000 reads (70.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2767102248982001310.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.7999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 15998 out of 20000 reads (79.99%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam403468520893219438.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.8999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 18000 out of 20000 reads (90.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17466106369015491334.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.9999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 19998 out of 20000 reads (99.99%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1939550475224246512.bam --STRATEGY HighAccuracy --PROBABILITY 0.3 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:53 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1808023038 to reproduce these results in the future. INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 6000 out of 20000 reads (30.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam500698719825746175.bam --STRATEGY HighAccuracy --PROBABILITY 0.4 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:53 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -117802561 to reproduce these results in the future. INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 8000 out of 20000 reads (40.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1117384543957611263.bam --STRATEGY HighAccuracy --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:53 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1505906095 to reproduce these results in the future. INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8189256579175353502.bam --STRATEGY HighAccuracy --PROBABILITY 0.6 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:53 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 2003449270 to reproduce these results in the future. INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 12000 out of 20000 reads (60.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:53 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1310152831607021153.bam --STRATEGY HighAccuracy --PROBABILITY 0.7 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:53 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -242762971 to reproduce these results in the future. INFO 2025-04-24 13:03:53 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:53 DownsampleSam Kept 14000 out of 20000 reads (70.00%). [Thu Apr 24 13:03:53 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16669187869194873331.bam --STRATEGY HighAccuracy --PROBABILITY 0.7999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:54 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1237727052 to reproduce these results in the future. INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 15998 out of 20000 reads (79.99%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10590018514698238571.bam --STRATEGY HighAccuracy --PROBABILITY 0.8999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:54 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 351050218 to reproduce these results in the future. INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 18000 out of 20000 reads (90.00%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9204417952530268921.bam --STRATEGY HighAccuracy --PROBABILITY 0.9999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:54 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1228037187 to reproduce these results in the future. INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 19998 out of 20000 reads (99.99%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4603343468116505788.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.3 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 6026 out of 20000 reads (30.13%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16655552197027207336.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.4 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 8002 out of 20000 reads (40.01%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6571544055396529721.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3396944687380223899.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.6 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 12002 out of 20000 reads (60.01%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7597589556262022622.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.7 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:54 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:54 DownsampleSam Kept 14018 out of 20000 reads (70.09%). [Thu Apr 24 13:03:54 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:54 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1356422130482849906.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.7999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 15972 out of 20000 reads (79.86%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13352438071966180477.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.8999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 18038 out of 20000 reads (90.19%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8795702423392324643.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.9999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 20000 out of 20000 reads (100.00%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7394184466283183752.bam --STRATEGY ConstantMemory --PROBABILITY 0.3 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1557241286 to reproduce these results in the future. INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 5824 out of 20000 reads (29.12%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3943388138887535580.bam --STRATEGY ConstantMemory --PROBABILITY 0.4 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1018056212 to reproduce these results in the future. INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 8056 out of 20000 reads (40.28%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9746741846758000581.bam --STRATEGY ConstantMemory --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 537210189 to reproduce these results in the future. INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 9884 out of 20000 reads (49.42%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam717392906731643031.bam --STRATEGY ConstantMemory --PROBABILITY 0.6 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1524340839 to reproduce these results in the future. INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 12022 out of 20000 reads (60.11%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18260808677662855952.bam --STRATEGY ConstantMemory --PROBABILITY 0.7 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1139502107 to reproduce these results in the future. INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 14040 out of 20000 reads (70.20%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6453214942221335752.bam --STRATEGY ConstantMemory --PROBABILITY 0.7999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -846223492 to reproduce these results in the future. INFO 2025-04-24 13:03:55 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:55 DownsampleSam Kept 15868 out of 20000 reads (79.34%). [Thu Apr 24 13:03:55 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:55 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16362470373645234534.bam --STRATEGY ConstantMemory --PROBABILITY 0.8999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:55 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 907019995 to reproduce these results in the future. INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 17900 out of 20000 reads (89.50%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16898744724954964723.bam --STRATEGY ConstantMemory --PROBABILITY 0.9999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:56 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -981235900 to reproduce these results in the future. INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 20000 out of 20000 reads (100.00%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3018464864912428135.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.3 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 5998 out of 20000 reads (29.99%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14495897664266447848.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.4 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 7998 out of 20000 reads (39.99%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6791357738502995817.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13252348446848761876.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.6 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 11998 out of 20000 reads (59.99%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam656417315678996597.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.7 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 14000 out of 20000 reads (70.00%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16598253649808701546.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.7999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 15998 out of 20000 reads (79.99%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10183984468916200093.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.8999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:56 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:56 DownsampleSam Kept 18000 out of 20000 reads (90.00%). [Thu Apr 24 13:03:56 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:56 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4876023762289134425.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.9999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 19998 out of 20000 reads (99.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam763032647635681102.bam --STRATEGY Chained --PROBABILITY 0.3 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1265587680 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 5998 out of 20000 reads (29.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6163927934415180508.bam --STRATEGY Chained --PROBABILITY 0.4 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 687677383 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 7998 out of 20000 reads (39.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4900695081974043709.bam --STRATEGY Chained --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -761168712 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9300651893042192266.bam --STRATEGY Chained --PROBABILITY 0.6 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -597395123 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 11998 out of 20000 reads (59.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7936638473222605408.bam --STRATEGY Chained --PROBABILITY 0.7 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1426725389 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 13998 out of 20000 reads (69.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11772168038884894121.bam --STRATEGY Chained --PROBABILITY 0.7999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1025495302 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 15998 out of 20000 reads (79.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6458293522924365980.bam --STRATEGY Chained --PROBABILITY 0.8999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1281597165 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 17998 out of 20000 reads (89.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17655532153365223430.bam --STRATEGY Chained --PROBABILITY 0.9999999999999999 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:57 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -2022341329 to reproduce these results in the future. INFO 2025-04-24 13:03:57 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:57 DownsampleSam Kept 19998 out of 20000 reads (99.99%). [Thu Apr 24 13:03:57 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:57 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18169580906470622995.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 10030 out of 20000 reads (50.15%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18169580906470622995.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4341912400711302192.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 4968 out of 10030 reads (49.53%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10747627578503117362.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 10142 out of 20000 reads (50.71%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10747627578503117362.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6558747852639371622.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:58 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:58 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 4988 out of 10142 reads (49.18%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7578985540268684454.bam --STRATEGY ConstantMemory --RANDOM_SEED 2147483647 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7578985540268684454.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8869874579033561344.bam --STRATEGY ConstantMemory --RANDOM_SEED 2147483647 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:58 DownsampleSam DownsampleSam has been run before on this data with the seed -1631654733. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:58 DownsampleSam RANDOM_SEED has been changed to -1631654733. INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 4918 out of 10000 reads (49.18%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3056500957764197234.bam --STRATEGY ConstantMemory --RANDOM_SEED -2147483648 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 9966 out of 20000 reads (49.83%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3056500957764197234.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13884425530070240450.bam --STRATEGY ConstantMemory --RANDOM_SEED -2147483648 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:58 DownsampleSam DownsampleSam has been run before on this data with the seed 1631269984. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:58 DownsampleSam RANDOM_SEED has been changed to 1631269984. INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 5034 out of 9966 reads (50.51%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13435884677781236322.bam --STRATEGY ConstantMemory --RANDOM_SEED -2147483648 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 9966 out of 20000 reads (49.83%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13435884677781236322.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17007362012829169665.bam --STRATEGY ConstantMemory --RANDOM_SEED 2147483647 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 4940 out of 9966 reads (49.57%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11941374368371602495.bam --STRATEGY ConstantMemory --RANDOM_SEED 2147483647 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11941374368371602495.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8953324481655622302.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 5052 out of 10000 reads (50.52%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6708591736703538481.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6708591736703538481.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9772450774510773586.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:58 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:58 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:03:58 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:58 DownsampleSam Kept 5108 out of 10018 reads (50.99%). [Thu Apr 24 13:03:58 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:58 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7400936942890080027.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7400936942890080027.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9939404508547529912.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:59 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 5102 out of 9998 reads (51.03%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1475090237111725645.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1475090237111725645.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18025559455044084200.bam --STRATEGY ConstantMemory --RANDOM_SEED 3 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 4932 out of 9998 reads (49.33%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8634556115687220001.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8634556115687220001.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4083728693193512699.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:59 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 5008 out of 10018 reads (49.99%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam971611186260865210.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam971611186260865210.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam15888800597021508753.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:59 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 4920 out of 10000 reads (49.20%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2844341593220294607.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2844341593220294607.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9754183776812093441.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 5008 out of 10018 reads (49.99%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12147423492616627023.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12147423492616627023.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10629099476535333623.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:59 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 4998 out of 9998 reads (49.99%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4173578754195112650.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4173578754195112650.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam15654475594740821650.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:03:59 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:03:59 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:59 DownsampleSam Kept 5000 out of 10000 reads (50.00%). [Thu Apr 24 13:03:59 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:03:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:03:59 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3579396480671073350.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3579396480671073350.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14093908635363761362.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 5000 out of 10000 reads (50.00%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6032033193162317921.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6032033193162317921.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8215677988926497249.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 4998 out of 9998 reads (49.99%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10385344391383391872.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10385344391383391872.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14270838767970521829.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 5008 out of 10018 reads (49.99%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14270838767970521829.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18129117069443336888.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:00 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 2526 out of 5008 reads (50.44%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18129117069443336888.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3066400618054054469.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 1262 out of 2526 reads (49.96%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3066400618054054469.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3033619791084954277.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 630 out of 1262 reads (49.92%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11054293912815359110.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11054293912815359110.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17577980098407437294.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 4970 out of 10000 reads (49.70%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17577980098407437294.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5768818751144320905.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:00 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 2510 out of 4970 reads (50.50%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5768818751144320905.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2092798693401824599.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:00 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:00 DownsampleSam RANDOM_SEED has been changed to 1260042744. INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 1298 out of 2510 reads (51.71%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2092798693401824599.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18171718025446488025.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 648 out of 1298 reads (49.92%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13125223931625674309.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 10030 out of 20000 reads (50.15%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13125223931625674309.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2919836295361275239.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 4968 out of 10030 reads (49.53%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2919836295361275239.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4159448205351404474.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 2484 out of 4968 reads (50.00%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4159448205351404474.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4858620223113762972.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:00 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 1242 out of 2484 reads (50.00%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4858620223113762972.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17810413788095692100.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 620 out of 1242 reads (49.92%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:00 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9966279050610863169.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:00 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:00 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:00 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9966279050610863169.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4101589830499825258.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 4920 out of 10000 reads (49.20%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4101589830499825258.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18268429020571771972.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 2458 out of 4920 reads (49.96%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18268429020571771972.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13692863421291096085.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 1228 out of 2458 reads (49.96%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13692863421291096085.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17770466044745163061.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 544 out of 1228 reads (44.30%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7001110907152220342.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 10142 out of 20000 reads (50.71%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7001110907152220342.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6293694010108075974.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 5070 out of 10142 reads (49.99%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6293694010108075974.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13993741330450054613.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 2562 out of 5070 reads (50.53%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13993741330450054613.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3030865268839957476.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam RANDOM_SEED has been changed to -723955400. INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 1304 out of 2562 reads (50.90%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3030865268839957476.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10006829495596424694.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 652 out of 1304 reads (50.00%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14123215730313533022.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 10142 out of 20000 reads (50.71%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14123215730313533022.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2056605546018221118.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 4988 out of 10142 reads (49.18%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2056605546018221118.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4610096351356648668.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 2494 out of 4988 reads (50.00%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4610096351356648668.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7696783123632679096.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 1246 out of 2494 reads (49.96%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7696783123632679096.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7413399538658266046.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 622 out of 1246 reads (49.92%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1541391612940300419.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1541391612940300419.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12706927285771001337.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 4998 out of 10000 reads (49.98%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12706927285771001337.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12207389203458150990.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 2516 out of 4998 reads (50.34%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12207389203458150990.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13248247333008962854.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 1214 out of 2516 reads (48.25%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13248247333008962854.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1092282735697196772.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:01 DownsampleSam RANDOM_SEED has been changed to -723955400. INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 626 out of 1214 reads (51.57%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14579900378917064772.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14579900378917064772.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2082779188506844157.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 4972 out of 9998 reads (49.73%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2082779188506844157.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13401971114959395093.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 2486 out of 4972 reads (50.00%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:01 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13401971114959395093.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16377380438792946919.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:01 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:01 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:01 DownsampleSam Kept 1276 out of 2486 reads (51.33%). [Thu Apr 24 13:04:01 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16377380438792946919.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13143208479496116748.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 646 out of 1276 reads (50.63%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13222957642913986152.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 10142 out of 20000 reads (50.71%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13222957642913986152.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2782269989334894599.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 5070 out of 10142 reads (49.99%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2782269989334894599.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5271089624337341930.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 2506 out of 5070 reads (49.43%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5271089624337341930.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8847358028136616128.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -723955400. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 1238 out of 2506 reads (49.40%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8847358028136616128.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1464835248914877188.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 642 out of 1238 reads (51.86%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam396283635939042794.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam396283635939042794.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7410096527324118300.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 5008 out of 10018 reads (49.99%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7410096527324118300.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17788335746002630838.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 2504 out of 5008 reads (50.00%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17788335746002630838.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17233217693316851652.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 1250 out of 2504 reads (49.92%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17233217693316851652.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16891902196235883055.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 610 out of 1250 reads (48.80%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3958091464242834020.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 10018 out of 20000 reads (50.09%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3958091464242834020.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1227964230161981324.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 5008 out of 10018 reads (49.99%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1227964230161981324.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4673329647763923059.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 2552 out of 5008 reads (50.96%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4673329647763923059.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12836546254847460939.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 1276 out of 2552 reads (50.00%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12836546254847460939.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7730984824890702162.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 638 out of 1276 reads (50.00%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10823091443673118808.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10823091443673118808.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4920194852776083404.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:02 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 4998 out of 10000 reads (49.98%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4920194852776083404.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1048888571659516880.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 2498 out of 4998 reads (49.98%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1048888571659516880.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11954919693376695981.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 1248 out of 2498 reads (49.96%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11954919693376695981.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11484824627030284457.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 624 out of 1248 reads (50.00%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13783200428194886247.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:02 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:02 DownsampleSam Kept 10030 out of 20000 reads (50.15%). [Thu Apr 24 13:04:02 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:02 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13783200428194886247.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1672973172489696750.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:02 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 5014 out of 10030 reads (49.99%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1672973172489696750.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18303152191947557198.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 2506 out of 5014 reads (49.98%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam18303152191947557198.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12571603161439116009.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 1236 out of 2506 reads (49.32%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam12571603161439116009.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9383596717728281356.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 618 out of 1236 reads (50.00%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8220366397826832084.bam --STRATEGY HighAccuracy --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8220366397826832084.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6344835121317390486.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 5044 out of 10000 reads (50.44%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6344835121317390486.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1600025998306729159.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 2520 out of 5044 reads (49.96%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam1600025998306729159.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4338733729333013209.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to 1260042744. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 1292 out of 2520 reads (51.27%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4338733729333013209.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17066873037943869126.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -423279216. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -423279216. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 644 out of 1292 reads (49.85%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14694611548413227886.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 9998 out of 20000 reads (49.99%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14694611548413227886.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14959040696735997503.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 4998 out of 9998 reads (49.99%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam14959040696735997503.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4677193127546444189.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 2466 out of 4998 reads (49.34%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4677193127546444189.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13602189096936913553.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 1232 out of 2466 reads (49.96%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13602189096936913553.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4333878052141888547.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to 1260042744. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 616 out of 1232 reads (50.00%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11165382716546010497.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11165382716546010497.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7148979166591722766.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 5080 out of 10000 reads (50.80%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7148979166591722766.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9445024926438176542.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 2540 out of 5080 reads (50.00%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9445024926438176542.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5037164323740899614.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 1270 out of 2540 reads (50.00%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5037164323740899614.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam16679753433842463374.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 634 out of 1270 reads (49.92%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6028661555597528931.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 10142 out of 20000 reads (50.71%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam6028661555597528931.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8132467301062406692.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 5070 out of 10142 reads (49.99%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8132467301062406692.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11221241539315597695.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 2534 out of 5070 reads (49.98%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11221241539315597695.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7918662765053949113.bam --STRATEGY Chained --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 1266 out of 2534 reads (49.96%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam7918662765053949113.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam15760950248499140394.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:03 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:03 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:03 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:03 DownsampleSam Kept 592 out of 1266 reads (46.76%). [Thu Apr 24 13:04:03 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:03 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4793154979204665830.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 10030 out of 20000 reads (50.15%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4793154979204665830.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam160689289942559456.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 5014 out of 10030 reads (49.99%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam160689289942559456.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9484309262462288547.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:04 DownsampleSam RANDOM_SEED has been changed to -1155484576. INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 2420 out of 5014 reads (48.26%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam9484309262462288547.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4852371814191341636.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 1198 out of 2420 reads (49.50%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam4852371814191341636.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5704351931575567352.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 598 out of 1198 reads (49.92%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13806301823833581680.bam --STRATEGY Chained --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam13806301823833581680.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17737287853397439883.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 5000 out of 10000 reads (50.00%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17737287853397439883.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam15494497268224833808.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 2544 out of 5000 reads (50.88%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam15494497268224833808.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3552570361517716785.bam --STRATEGY HighAccuracy --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 1272 out of 2544 reads (50.00%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam3552570361517716785.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam5735897745875625687.bam --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:04 DownsampleSam RANDOM_SEED has been changed to -1155869325. INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 630 out of 1272 reads (49.53%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam11908593774750666389.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10170171127294352888.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 10000 out of 20000 reads (50.00%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10170171127294352888.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2860496972793231844.bam --STRATEGY HighAccuracy --RANDOM_SEED 1 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 5000 out of 10000 reads (50.00%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam2860496972793231844.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17617098183924284995.bam --STRATEGY ConstantMemory --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 2434 out of 5000 reads (48.68%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam17617098183924284995.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8492502308433409277.bam --STRATEGY ConstantMemory --RANDOM_SEED 0 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 1256 out of 2434 reads (51.60%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:04 EDT 2025] DownsampleSam --INPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam8492502308433409277.bam --OUTPUT file:/tmp/ds_test_Downsampling17084071135015241114/DownsampleSam10426745539556028201.bam --STRATEGY Chained --RANDOM_SEED 2 --PROBABILITY 0.5 --CREATE_INDEX true --ACCURACY 1.0E-4 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2025-04-24 13:04:04 DownsampleSam RANDOM_SEED has been changed to -1154715079. INFO 2025-04-24 13:04:04 DownsampleSam Finished downsampling. INFO 2025-04-24 13:04:04 DownsampleSam Kept 614 out of 1256 reads (48.89%). [Thu Apr 24 13:04:04 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 WARNING 2025-04-24 13:04:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.