Class picard.sam.CompareSAMsTest

all > picard.sam > CompareSAMsTest

tests

failures

ignored

0.665s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)	0.019s	passed
testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)	0.018s	passed
testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)	0.019s	passed
testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)	0.019s	passed
testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)	0.018s	passed
testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)	0.017s	passed
testComparisons[15](unsorted.sam, unsorted.sam, null, true)	0.018s	passed
testComparisons[16](unsorted.sam, unsorted2.sam, null, false)	0.018s	passed
testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)	0.022s	passed
testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.017s	passed
testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.015s	passed
testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)	0.017s	passed
testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.014s	passed
testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)	0.013s	passed
testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)	0.013s	passed
testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.012s	passed
testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.012s	passed
testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.012s	passed
testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)	0.012s	passed
testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)	0.012s	passed
testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)	0.013s	passed
testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)	0.011s	passed
testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)	0.016s	passed
testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)	0.016s	passed
testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)	0.017s	passed
testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)	0.018s	passed
testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)	0.018s	passed
testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)	0.018s	passed
testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)	0.017s	passed
testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)	0.018s	passed
testMQConcordance[0](genomic_sorted.sam, unsorted.sam, null)	0.006s	passed
testMQConcordance[10](genomic_sorted.sam, unmapped_second.sam, [[Ljava.lang.Object;@6f71453e)	0.007s	passed
testMQConcordance[11](unmapped_first.sam, unmapped_second.sam, [[Ljava.lang.Object;@438cfb75)	0.007s	passed
testMQConcordance[12](unmapped_first.sam, unmapped_first.sam, [[Ljava.lang.Object;@3e01dd50)	0.006s	passed
testMQConcordance[13](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, [[Ljava.lang.Object;@35d7dcf5)	0.006s	passed
testMQConcordance[14](unsorted.sam, unsorted.sam, [[Ljava.lang.Object;@20d4276b)	0.007s	passed
testMQConcordance[15](unsorted.sam, unsorted2.sam, [[Ljava.lang.Object;@878046f)	0.006s	passed
testMQConcordance[16](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [[Ljava.lang.Object;@302b88e4)	0.006s	passed
testMQConcordance[17](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [[Ljava.lang.Object;@292db884)	0.007s	passed
testMQConcordance[18](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [[Ljava.lang.Object;@2b4611e3)	0.006s	passed
testMQConcordance[19](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [[Ljava.lang.Object;@423ebd8c)	0.006s	passed
testMQConcordance[1](genomic_sorted.sam, chr21.sam, null)	0.006s	passed
testMQConcordance[20](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [[Ljava.lang.Object;@681e425e)	0.007s	passed
testMQConcordance[21](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [[Ljava.lang.Object;@17e13730)	0.007s	passed
testMQConcordance[22](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [[Ljava.lang.Object;@5aa6eb4)	0.006s	passed
testMQConcordance[23](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [[Ljava.lang.Object;@a669486)	0.007s	passed
testMQConcordance[24](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [[Ljava.lang.Object;@1ee17469)	0.006s	passed
testMQConcordance[25](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [[Ljava.lang.Object;@4d3bafdb)	0.007s	passed
testMQConcordance[26](genomic_sorted.sam, mq0_2.sam, [[Ljava.lang.Object;@e6da5ca)	0.006s	passed
testMQConcordance[27](mq0_1.sam, mq0_2.sam, [[Ljava.lang.Object;@3fff664c)	0.007s	passed
testMQConcordance[2](genomic_sorted.sam, bigger_seq_dict.sam, null)	0.006s	passed
testMQConcordance[3](genomic_sorted.sam, genomic_sorted.sam, [[Ljava.lang.Object;@17456db)	0.008s	passed
testMQConcordance[4](genomic_sorted.sam, has_non_primary.sam, [[Ljava.lang.Object;@82a1e26)	0.007s	passed
testMQConcordance[5](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, [[Ljava.lang.Object;@3cc87568)	0.007s	passed
testMQConcordance[6](group_same_coord.sam, group_same_coord_diff_order.sam, [[Ljava.lang.Object;@116e376e)	0.007s	passed
testMQConcordance[7](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, [[Ljava.lang.Object;@652e2809)	0.007s	passed
testMQConcordance[8](group_same_coord.sam, diff_coords.sam, [[Ljava.lang.Object;@658959be)	0.008s	passed
testMQConcordance[9](genomic_sorted.sam, unmapped_first.sam, [[Ljava.lang.Object;@9df1ca)	0.007s	passed

Standard output

Sort order differs.
File 1: coordinate
File 2: null
Sort Order differs.
File 1: coordinate
File 2: unsorted
Cannot compare alignments if sort orders differ.
SAM files differ.
Sort order differs.
File 1: null
File 2: coordinate
Sort Order differs.
File 1: unsorted
File 2: coordinate
Cannot compare alignments if sort orders differ.
SAM files differ.
Name of sequence record 1 differs.
File 1: chr20
File 2: chr21
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
SAM files differ.
Name of sequence record 1 differs.
File 1: chr21
File 2: chr20
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
SAM files differ.
Length of sequence dictionaries differs.
File 1: 1
File 2: 2
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
SAM files differ.
Length of sequence dictionaries differs.
File 1: 2
File 2: 1
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
SAM files differ.
SAM files match.
SAM files match.
SAM files match.
SAM files match.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files match.
SAM files match.
File format version differs.
File 1: 1.0
File 2: 1.6
SAM files differ.
File format version differs.
File 1: 1.6
File 2: 1.0
SAM files differ.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
Sort order differs.
File 1: coordinate
File 2: null
Sort Order differs.
File 1: coordinate
File 2: unsorted
Cannot compare alignments if sort orders differ.
SAM files differ.
Name of sequence record 1 differs.
File 1: chr20
File 2: chr21
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
SAM files differ.
Length of sequence dictionaries differs.
File 1: 1
File 2: 2
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
SAM files differ.
SAM files match.
SAM files match.
SAM files differ.
SAM files differ.
SAM files match.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files match.
File format version differs.
File 1: 1.0
File 2: 1.6
SAM files differ.
SAM files match.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.
SAM files differ.

Standard error

[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam --OUTPUT /tmp/compareSam15093955639741742932.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam15093955639741742932.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/chr21.sam --OUTPUT /tmp/compareSam1801882396948873059.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/chr21.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam1801882396948873059.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam --OUTPUT /tmp/compareSam4051134954315450786.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam4051134954315450786.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam --OUTPUT /tmp/compareSam14961589786257803856.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam --OUTPUT /tmp/compareSam14961589786257803856.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam8890848237144138815.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam8890848237144138815.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/has_non_primary.sam --OUTPUT /tmp/compareSam11391177402609840620.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/has_non_primary.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam11391177402609840620.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam --OUTPUT /tmp/compareSam10228420832601750440.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam --OUTPUT /tmp/compareSam10228420832601750440.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam --OUTPUT /tmp/compareSam16141279966871011017.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam --OUTPUT /tmp/compareSam16141279966871011017.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam --OUTPUT /tmp/compareSam4427219373967394666.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam --OUTPUT /tmp/compareSam4427219373967394666.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/diff_coords.sam --OUTPUT /tmp/compareSam4622575572540819240.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/diff_coords.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam --OUTPUT /tmp/compareSam4622575572540819240.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam --OUTPUT /tmp/compareSam6634406803430691891.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam6634406803430691891.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam --OUTPUT /tmp/compareSam11222260934973740933.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam11222260934973740933.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam --OUTPUT /tmp/compareSam10598337902876948196.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam --OUTPUT /tmp/compareSam10598337902876948196.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam --OUTPUT /tmp/compareSam16976219858061866556.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam --OUTPUT /tmp/compareSam16976219858061866556.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam --OUTPUT /tmp/compareSam1954417700286963282.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam1954417700286963282.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam --OUTPUT /tmp/compareSam381277875582960413.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam --OUTPUT /tmp/compareSam381277875582960413.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted2.sam --OUTPUT /tmp/compareSam5193178194377321749.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:46 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 13:03:46 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted2.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam --OUTPUT /tmp/compareSam5193178194377321749.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam --OUTPUT /tmp/compareSam14145969450077481106.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam --OUTPUT /tmp/compareSam14145969450077481106.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam --OUTPUT /tmp/compareSam12023072668455142563.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam --OUTPUT /tmp/compareSam12023072668455142563.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam --OUTPUT /tmp/compareSam15394728884201072262.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam --OUTPUT /tmp/compareSam15394728884201072262.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam --OUTPUT /tmp/compareSam14320138646677052496.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam --OUTPUT /tmp/compareSam14320138646677052496.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam --OUTPUT /tmp/compareSam3356940889397442910.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam --OUTPUT /tmp/compareSam3356940889397442910.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam --OUTPUT /tmp/compareSam12176215772833579851.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam --OUTPUT /tmp/compareSam12176215772833579851.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam --OUTPUT /tmp/compareSam6059221175151930240.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam --OUTPUT /tmp/compareSam6059221175151930240.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam --OUTPUT /tmp/compareSam802897547906834617.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam --OUTPUT /tmp/compareSam802897547906834617.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam --OUTPUT /tmp/compareSam9909635354243560676.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam --OUTPUT /tmp/compareSam9909635354243560676.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam --OUTPUT /tmp/compareSam8402796634948236045.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam --OUTPUT /tmp/compareSam8402796634948236045.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam --OUTPUT /tmp/compareSam8295098023671152433.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam8295098023671152433.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_1.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam --OUTPUT /tmp/compareSam12951477902035104083.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_1.sam --OUTPUT /tmp/compareSam12951477902035104083.tsv --LENIENT_DUP true --LENIENT_LOW_MQ_ALIGNMENT true --LENIENT_HEADER false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_1.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam --OUTPUT /tmp/compareSam9870533403854838395.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_1.sam --OUTPUT /tmp/compareSam9870533403854838395.tsv --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --COMPARE_MQ 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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam --OUTPUT /tmp/compareSam8902160860349598092.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/chr21.sam --OUTPUT /tmp/compareSam10269260741304882778.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam --OUTPUT /tmp/compareSam2895657770068525505.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam --OUTPUT /tmp/compareSam12741742842322008526.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/has_non_primary.sam --OUTPUT /tmp/compareSam5681336164401466792.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam --OUTPUT /tmp/compareSam1573402986611410614.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam --OUTPUT /tmp/compareSam70077169112100338.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam --OUTPUT /tmp/compareSam17132440493164492058.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/diff_coords.sam --OUTPUT /tmp/compareSam8798014768047075948.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam --OUTPUT /tmp/compareSam5192773042019700490.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam --OUTPUT /tmp/compareSam10322125165682626308.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam --OUTPUT /tmp/compareSam8957942456080586232.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam --OUTPUT /tmp/compareSam14582721349210052325.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam --OUTPUT /tmp/compareSam3599487046465821732.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam --OUTPUT /tmp/compareSam15746111436057782338.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/unsorted2.sam --OUTPUT /tmp/compareSam5702641621872769555.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam --OUTPUT /tmp/compareSam10740764094196653977.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam --OUTPUT /tmp/compareSam14908339180812597137.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam --OUTPUT /tmp/compareSam14813365120830866245.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam --OUTPUT /tmp/compareSam2370707769205736721.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam --OUTPUT /tmp/compareSam15236187178295303708.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam --OUTPUT /tmp/compareSam8818424472309446526.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam --OUTPUT /tmp/compareSam8138165047703816991.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam --OUTPUT /tmp/compareSam12620150720924974627.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam --OUTPUT /tmp/compareSam12388438297446441843.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam --OUTPUT /tmp/compareSam8888125178147620436.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam --OUTPUT /tmp/compareSam17890478535997437298.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:03:47 EDT 2025] CompareSAMs /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_1.sam /mounts/lovelace/software/picard/picard/testdata/picard/sam/CompareSAMs/mq0_2.sam --OUTPUT /tmp/compareSam9280951361237030903.tsv --COMPARE_MQ true --LENIENT_HEADER false --LENIENT_DUP false --LENIENT_LOW_MQ_ALIGNMENT false --LENIENT_UNKNOWN_MQ_ALIGNMENT false --LOW_MQ_THRESHOLD 3 --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 13:03:47 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 13:03:47 EDT 2025] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp