Class picard.sam.SamToFastqTest

all > picard.sam > SamToFastqTest
24

tests
0

failures
0

ignored
0.180s

duration
100%

successful

Tests

Test Duration Result
testBadFile[0](bad/unpaired-mate.sam) 0.013s passed
testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam) 0.009s passed
testBadGroupedFile[0](bad/grouped-unpaired-mate.sam) 0.009s passed
testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test) 0.009s passed
testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test) 0.008s passed
testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test) 0.008s passed
testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test) 0.008s passed
testFileCompression[0](ok/sorted-pair.sam) 0.009s passed
testFileCompression[1](ok/sorted-pair-no-rg.sam) 0.007s passed
testFileCompression[2](ok/last-pair-mates-flipped.sam) 0.008s passed
testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam) 0.006s passed
testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam) 0.006s passed
testMissingRgFile[0](bad/missing-rg-info.sam) 0.011s passed
testOkFile[0](ok/sorted-pair.sam) 0.007s passed
testOkFile[1](ok/sorted-pair-no-rg.sam) 0.006s passed
testOkFile[2](ok/last-pair-mates-flipped.sam) 0.007s passed
testOkFile[3](ok/first-mate-bof-last-mate-eof.sam) 0.006s passed
testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@749a0457) 0.007s passed
testOkInterleavedFile[0](ok/sorted-pair.sam) 0.006s passed
testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam) 0.006s passed
testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam) 0.006s passed
testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam) 0.006s passed
testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8) 0.006s passed
testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8) 0.006s passed

Standard error

[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam --FASTQ /tmp/tt-pair1.17532254777355782336.fastq --SECOND_END_FASTQ /tmp/tt-pair2.9099259960202252098.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam --FASTQ /tmp/pair12025899720020342118.fastq --SECOND_END_FASTQ /tmp/pair212663708355424497729.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam --OUTPUT_PER_RG true --OUTPUT_DIR /tmp/root --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam --FASTQ /tmp/clippingtest12001468097057898161fastq --SECOND_END_FASTQ /tmp/clippingtest23032150922341023219fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam --FASTQ /tmp/clippingtest1722086001059336867fastq --SECOND_END_FASTQ /tmp/clippingtest24560907021532161001fastq --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION X --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam --FASTQ /tmp/clippingtest18525887595055471320fastq --SECOND_END_FASTQ /tmp/clippingtest2720497214677049387fastq --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION N --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam --FASTQ /tmp/clippingtest15776662116398728229fastq --SECOND_END_FASTQ /tmp/clippingtest21897660246617070075fastq --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam --FASTQ /tmp/pair19313715405513843570.fastq.gz --SECOND_END_FASTQ /tmp/pair214423362415260541463.fastq.gz --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam --FASTQ /tmp/pair11021074300526453201.fastq.gz --SECOND_END_FASTQ /tmp/pair28176615897287538995.fastq.gz --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam --FASTQ /tmp/pair16372285009883480080.fastq.gz --SECOND_END_FASTQ /tmp/pair25089640563233683706.fastq.gz --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam --FASTQ /tmp/pair115450854740619980260.fastq.gz --SECOND_END_FASTQ /tmp/pair23193281618951776187.fastq.gz --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam --FASTQ /tmp/pair19212973304423068254.fastq --SECOND_END_FASTQ /tmp/pair217655420701043403199.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam --OUTPUT_PER_RG true --OUTPUT_DIR /tmp/root --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam --FASTQ /tmp/pair13083532821143189222.fastq --SECOND_END_FASTQ /tmp/pair214379277539965608057.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam --FASTQ /tmp/pair116182095872920385125.fastq --SECOND_END_FASTQ /tmp/pair2654238331917301748.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam --FASTQ /tmp/pair14302493064415037412.fastq --SECOND_END_FASTQ /tmp/pair21378658472121578558.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam --FASTQ /tmp/pair116418392938744858868.fastq --SECOND_END_FASTQ /tmp/pair216464778302483961769.fastq --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam --OUTPUT_PER_RG true --OUTPUT_DIR /tmp/root --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam --FASTQ /tmp/pair12992313566180560172.fastq --INTERLEAVE true --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam --FASTQ /tmp/pair17836519741552356638.fastq --INTERLEAVE true --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam --FASTQ /tmp/pair16079291289571063767.fastq --INTERLEAVE true --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam --FASTQ /tmp/pair10041774725635747655.fastq --INTERLEAVE true --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --READ1_TRIM 0 --READ2_TRIM 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam --FASTQ /tmp/pair116435416121463315858.fastq --SECOND_END_FASTQ /tmp/pair216287599047552069785.fastq --READ1_TRIM 6 --READ1_MAX_BASES_TO_WRITE 7 --READ2_TRIM 5 --READ2_MAX_BASES_TO_WRITE 8 --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:15 EDT 2025] SamToFastq --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam --FASTQ /tmp/pair117036581773471517810.fastq --SECOND_END_FASTQ /tmp/pair216729224312002596413.fastq --READ1_TRIM 7 --READ1_MAX_BASES_TO_WRITE 7 --READ2_TRIM 3 --READ2_MAX_BASES_TO_WRITE 8 --OUTPUT_PER_RG false --COMPRESS_OUTPUTS_PER_RG false --RG_TAG PU --RE_REVERSE true --INTERLEAVE false --INCLUDE_NON_PF_READS false --CLIPPING_MIN_LENGTH 0 --INCLUDE_NON_PRIMARY_ALIGNMENTS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:15 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:15 EDT 2025] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824