Class picard.sam.FastqToSamTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| readPairNameBad[0](, ) | 0.001s | passed |
| readPairNameBad[1](aa/1, bb/2) | 0s | passed |
| readPairNameBad[2](aa, bb) | 0s | passed |
| readPairNameBad[3](aa/1, aa) | 0s | passed |
| readPairNameBad[4](aa, aa/2) | 0s | passed |
| readPairNameBad[5](aa/1, aa/1) | 0s | passed |
| readPairNameBad[6](aa/2, aa/2) | 0s | passed |
| readPairNameOk[0](aa/1, aa/2) | 0s | passed |
| readPairNameOk[10](aa/, aa/) | 0s | passed |
| readPairNameOk[11](ab/c, ab/c) | 0s | passed |
| readPairNameOk[1](aa, aa) | 0s | passed |
| readPairNameOk[2](aa/bb, aa/bb) | 0s | passed |
| readPairNameOk[3](aa/bb/, aa/bb/) | 0s | passed |
| readPairNameOk[4](aa/bb/1, aa/bb/2) | 0s | passed |
| readPairNameOk[5](aa/bb/cc/dd/ee/ff/1, aa/bb/cc/dd/ee/ff/2) | 0s | passed |
| readPairNameOk[6](////1, ////2) | 0s | passed |
| readPairNameOk[7](/, /) | 0s | passed |
| readPairNameOk[8](////, ////) | 0s | passed |
| readPairNameOk[9](/aa, /aa) | 0s | passed |
| testBadFile[0](bad-format/bad-qual-header.txt) | 0.008s | passed |
| testBadFile[1](bad-format/bad-seq-header.txt) | 0.007s | passed |
| testBadFile[2](bad-format/extra-line.txt) | 0.006s | passed |
| testBadFile[3](bad-format/too-many-quals.txt) | 0.006s | passed |
| testBadFile[4](bad-format/1lines.txt) | 0.006s | passed |
| testBadFile[5](bad-format/2lines.txt) | 0.006s | passed |
| testBadFile[6](bad-format/3lines.txt) | 0.005s | passed |
| testEmptyFastq | 0.006s | passed |
| testEmptyFastqAllowed | 0.006s | passed |
| testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina) | 0.006s | passed |
| testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina) | 0.006s | passed |
| testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq.gz, Standard) | 0.161s | passed |
| testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard) | 0.184s | passed |
| testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard) | 0.010s | passed |
| testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa) | 0.008s | passed |
| testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa) | 0.006s | passed |
| testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina) | 0.006s | passed |
| testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina) | 0.007s | passed |
| testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina) | 0.006s | passed |
| testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt) | 0.007s | passed |
| testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt) | 0.006s | passed |
| testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt) | 0.006s | passed |
| testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt) | 0.007s | passed |
| testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt) | 0.006s | passed |
| testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt) | 0.006s | passed |
| testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard) | 0.005s | passed |
| testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina) | 0.005s | passed |
| testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard) | 0.005s | passed |
| testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina) | 0.006s | passed |
| testPermissiveFail[2](permissive-format/pair1.txt, null, Standard) | 0.005s | passed |
| testPermissiveFail[3](permissive-format/pair2.txt, null, Standard) | 0.006s | passed |
| testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina) | 0.005s | passed |
| testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina) | 0.006s | passed |
| testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina) | 0.005s | passed |
| testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard) | 0.005s | passed |
| testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina) | 0.007s | passed |
| testPermissiveOk[2](permissive-format/pair1.txt, null, Standard) | 0.006s | passed |
| testPermissiveOk[3](permissive-format/pair2.txt, null, Standard) | 0.006s | passed |
| testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina) | 0.006s | passed |
| testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina) | 0.005s | passed |
| testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina) | 0.005s | passed |
| testSequentialFiles | 0.024s | passed |
| testStreamInput | 1.012s | passed |
| testStreamInputWithoutQuality | 0.009s | passed |
Standard error
[Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/bad-qual-header.txt4589067540964442655.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/bad-seq-header.txt17334214943326640702.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/extra-line.txt6954942614220644255.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/too-many-quals.txt14316531976656977951.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/1lines.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/1lines.txt4270994534740436496.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/2lines.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/2lines.txt3083732839906233688.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-format/3lines.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/3lines.txt12147836627261805005.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /tmp/empty10138106664928462949.fastq --QUALITY_FORMAT Illumina --OUTPUT /tmp/empty10138106664928462949.fastq2430773318007483843.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /tmp/empty2655655076899510129.fastq --QUALITY_FORMAT Illumina --OUTPUT /tmp/empty2655655076899510129.fastq17213948444970646172.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_EMPTY_FASTQ true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:04 FastqToSam Input FASTQ is empty, will write out SAM/BAM file with no reads. INFO 2025-04-24 13:04:04 FastqToSam Processed 0 fastq reads [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq --QUALITY_FORMAT Illumina --OUTPUT /tmp/sanger_full_range_as_sanger-63.fastq17904594443040497373.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_sequence.txt5835770636678791251.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq.gz --QUALITY_FORMAT Standard --OUTPUT /tmp/5k-v1-Rhodobacter_LW1.sam.fastq.gz18047388669014726780.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:04 FastqToSam Processed 5000 fastq reads [Thu Apr 24 13:04:04 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:04 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq --QUALITY_FORMAT Standard --OUTPUT /tmp/5k-30BB2AAXX.3.aligned.sam.fastq8459107054159138837.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:04 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:04 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:04 FastqToSam Processed 4952 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq --QUALITY_FORMAT Standard --OUTPUT /tmp/sanger_full_range_as_sanger-63.fastq277348478883471696.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt --QUALITY_FORMAT Solexa --OUTPUT /tmp/s_1_sequence.txt815393067953208104.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Solexa. INFO 2025-04-24 13:04:05 FastqToSam Processed 25 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq --QUALITY_FORMAT Solexa --OUTPUT /tmp/solexa_full_range_as_solexa.fastq1304560182314548631.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Solexa. INFO 2025-04-24 13:04:05 FastqToSam Processed 2 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_2_sequence.txt14590407385997861323.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_2_sequence.txt6834423815532491855.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_sequence.txt2546989577943232192.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt10034395386507717656.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1-one-more-record.txt17817844942935901259.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt12828953054665461062.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1-badnum.txt1351551281026389980.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1-nonum.txt10246634087361924248.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1-onetoken.txt4058637058960547980.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt1671902564461020307.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:05 FastqToSam Processed 5 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_1_sequence.txt9647201271126115634.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt10329237937214553378.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_1_sequence.txt4973706412742143856.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt14079927719858591468.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair2.txt5277723340375280512.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_1_sequence.txt13607322449855102497.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_2_sequence.txt2591158830268432971.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_sequence.txt17171368109415950650.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_AND_IGNORE_EMPTY_LINES false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt3310520468604987970.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:05 FastqToSam Processed 5 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_1_sequence.txt433792907817361142.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair1.txt3518422995097501674.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:05 FastqToSam Processed 5 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt --QUALITY_FORMAT Standard --OUTPUT /tmp/pair2.txt3683671735026512970.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:04:05 FastqToSam Processed 5 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_1_sequence.txt14363018559257716336.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_2_sequence.txt3129715105576932131.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt --QUALITY_FORMAT Illumina --OUTPUT /tmp/s_1_sequence.txt844089189296884351.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 10 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq --QUALITY_FORMAT Illumina --OUTPUT /tmp/single_end_R1_001.fastq7065247371633622783.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq --USE_SEQUENTIAL_FASTQS true --QUALITY_FORMAT Illumina --OUTPUT /tmp/single_end_R1_001.fastq3273113077035064935.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq --QUALITY_FORMAT Illumina --OUTPUT /tmp/paired_end_R1_001.fastq15841708093218018836.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --USE_SEQUENTIAL_FASTQS false --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:05 EDT 2025] FastqToSam --FASTQ /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq --FASTQ2 /mounts/lovelace/software/picard/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq --USE_SEQUENTIAL_FASTQS true --QUALITY_FORMAT Illumina --OUTPUT /tmp/paired_end_R1_001.fastq5803898658544929035.sam --READ_GROUP_NAME rg --SAMPLE_NAME s1 --ALLOW_AND_IGNORE_EMPTY_LINES true --SORT_ORDER queryname --MIN_Q 0 --MAX_Q 93 --STRIP_UNPAIRED_MATE_NUMBER false --ALLOW_EMPTY_FASTQ 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 13:04:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:05 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2025-04-24 13:04:05 FastqToSam Auto-detected quality format as: Illumina. INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads INFO 2025-04-24 13:04:05 FastqToSam Processed 1 fastq reads [Thu Apr 24 13:04:05 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824