Class picard.sam.SplitSamByNumberOfReadsTest
Tests
| Test |
Duration |
Result |
| testNFiles |
0.023s |
passed |
| testNoTotalReads |
0.018s |
passed |
| testOkFile |
0.017s |
passed |
| testOneOutput |
0.011s |
passed |
| testOutPrefixWithZeros |
0.016s |
passed |
| testStreamWithoutTotalReads |
0.005s |
passed |
| testThreeReadTemplate |
0.017s |
passed |
| testWrongTotalReads |
0.017s |
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
Standard error
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam --SPLIT_TO_N_FILES 2 --TOTAL_READS_IN_INPUT 10 --OUTPUT /tmp/temp_dir7516794409638394463 --SPLIT_TO_N_READS 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir7516794409638394463/shard_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir7516794409638394463/shard_0002.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam --SPLIT_TO_N_READS 5 --OUTPUT /tmp/temp_dir423426977132757282 --SPLIT_TO_N_FILES 0 --TOTAL_READS_IN_INPUT 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version.
INFO 2025-04-24 13:04:15 SplitSamByNumberOfReads First pass traversal to count number of reads is beginning. If number of reads is known, use TOTAL_READS_IN_INPUT to skip first traversal.
INFO 2025-04-24 13:04:15 SplitSamByNumberOfReads First pass traversal to count number of reads ended, found 10 total reads.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir423426977132757282/shard_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir423426977132757282/shard_0002.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam --SPLIT_TO_N_READS 5 --TOTAL_READS_IN_INPUT 10 --OUTPUT /tmp/temp_dir17482418485286738902 --SPLIT_TO_N_FILES 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir17482418485286738902/shard_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir17482418485286738902/shard_0002.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam --SPLIT_TO_N_READS 10 --TOTAL_READS_IN_INPUT 10 --OUTPUT /tmp/temp_dir14536800365237206063 --SPLIT_TO_N_FILES 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir14536800365237206063/shard_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam --SPLIT_TO_N_READS 5 --OUTPUT /tmp/temp_dir13460564267405822100 --OUT_PREFIX Sample01 --SPLIT_TO_N_FILES 0 --TOTAL_READS_IN_INPUT 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version.
INFO 2025-04-24 13:04:15 SplitSamByNumberOfReads First pass traversal to count number of reads is beginning. If number of reads is known, use TOTAL_READS_IN_INPUT to skip first traversal.
INFO 2025-04-24 13:04:15 SplitSamByNumberOfReads First pass traversal to count number of reads ended, found 10 total reads.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir13460564267405822100/Sample01_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir13460564267405822100/Sample01_0002.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT /dev/stdin --SPLIT_TO_N_READS 5 --OUTPUT /tmp/temp_dir12843442743999913389 --SPLIT_TO_N_FILES 0 --TOTAL_READS_IN_INPUT 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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
ERROR 2025-04-24 13:04:15 SplitSamByNumberOfReads INPUT is not a regular file: /dev/stdin. If TOTAL_READS_IN_INPUT is not supplied, INPUT cannot be a stream.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-triplet.sam --SPLIT_TO_N_READS 2 --TOTAL_READS_IN_INPUT 11 --OUTPUT /tmp/temp_dir13151716413056132104 --SPLIT_TO_N_FILES 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir13151716413056132104/shard_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir13151716413056132104/shard_0002.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SplitSamByNumberOfReads --INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam --SPLIT_TO_N_READS 5 --TOTAL_READS_IN_INPUT 20 --OUTPUT /tmp/temp_dir14692743050344096865 --SPLIT_TO_N_FILES 0 --OUT_PREFIX shard --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version.
WARNING 2025-04-24 13:04:15 SplitSamByNumberOfReads The totalReads (20) provided does not match the reads found in the input file (10). Files may not be split evenly or number of files may not match what was requested. There were 2 files generated each with around 5 reads except the last file which contained 4 reads.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir14692743050344096865/shard_0001.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] ValidateSamFile --INPUT /tmp/temp_dir14692743050344096865/shard_0002.sam --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 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 13:04:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824