Class picard.sam.CramCompatibilityTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testShouldFailWhenCRAMWithoutReference[0](picard.sam.AddOrReplaceReadGroups, RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.027s | passed |
| testShouldFailWhenCRAMWithoutReference[10](picard.sam.GatherBamFiles, I=/mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/test_cram_file_query_sorted.cram) | 0.011s | passed |
| testShouldFailWhenCRAMWithoutReference[11](picard.sam.markduplicates.MarkDuplicatesWithMateCigar, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicatesWithMateCigar2726957274460643193.txt, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.017s | passed |
| testShouldFailWhenCRAMWithoutReference[12](picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/SimpleMarkDuplicatesWithMateCigar8586421587152559285.txt, testdata/picard/sam/MarkDuplicates/one_pair_mc.cram) | 0.005s | passed |
| testShouldFailWhenCRAMWithoutReference[13](picard.illumina.MarkIlluminaAdapters, METRICS=/tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters4745769828291703904.txt, testdata/picard/sam/test_cram_file_query_sorted.cram) | 0.010s | passed |
| testShouldFailWhenCRAMWithoutReference[14](picard.sam.SplitSamByLibrary, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.012s | passed |
| testShouldFailWhenCRAMWithoutReference[1](picard.sam.CleanSam, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.019s | passed |
| testShouldFailWhenCRAMWithoutReference[2](picard.sam.DownsampleSam, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.021s | passed |
| testShouldFailWhenCRAMWithoutReference[3](picard.sam.FixMateInformation, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.017s | passed |
| testShouldFailWhenCRAMWithoutReference[4](picard.sam.markduplicates.MarkDuplicates, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicates1117559000146991501.dir, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.139s | passed |
| testShouldFailWhenCRAMWithoutReference[5](picard.sam.MergeSamFiles, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.025s | passed |
| testShouldFailWhenCRAMWithoutReference[6](picard.sam.PositionBasedDownsampleSam, FRACTION=0.5, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.019s | passed |
| testShouldFailWhenCRAMWithoutReference[7](picard.sam.SortSam, SORT_ORDER=queryname, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.017s | passed |
| testShouldFailWhenCRAMWithoutReference[8](picard.sam.ReplaceSamHeader, HEADER=testdata/picard/sam/test_cram_file_header_only.cram, testdata/picard/sam/test_cram_file_coordinate_sorted.cram) | 0.016s | passed |
| testShouldFailWhenCRAMWithoutReference[9](picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar, null, testdata/picard/sam/test_cram_file_query_sorted.cram) | 0.010s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[0](picard.sam.AddOrReplaceReadGroups, RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.086s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[10](picard.sam.GatherBamFiles, I=/mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/test_cram_file_query_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.066s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[11](picard.sam.markduplicates.MarkDuplicatesWithMateCigar, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicatesWithMateCigar847294910959987490.txt, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.070s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[12](picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/SimpleMarkDuplicatesWithMateCigar10811745762715745254.txt, testdata/picard/sam/MarkDuplicates/one_pair_mc.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.023s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[13](picard.sam.ReorderSam, SEQUENCE_DICTIONARY=testdata/picard/sam/test_cram_file.ref.fa, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.208s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[14](picard.sam.SetNmMdAndUqTags, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.060s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[15](picard.sam.MergeBamAlignment, UNMAPPED=/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.cram ALIGNED=/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.cram, null, testdata/picard/sam/MergeBamAlignment/cliptest.fasta) | 0.037s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[16](picard.illumina.MarkIlluminaAdapters, METRICS=/tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters14016845742977392570.txt, testdata/picard/sam/test_cram_file_query_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.054s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[17](picard.sam.SplitSamByLibrary, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.085s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[1](picard.sam.CleanSam, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.053s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[2](picard.sam.DownsampleSam, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.040s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[3](picard.sam.FixMateInformation, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.329s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[4](picard.sam.markduplicates.MarkDuplicates, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicates15160830643134469511.dir, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 1.029s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[5](picard.sam.MergeSamFiles, null, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.091s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[6](picard.sam.PositionBasedDownsampleSam, FRACTION=0.5, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.044s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[7](picard.sam.SortSam, SORT_ORDER=queryname, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.188s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[8](picard.sam.ReplaceSamHeader, HEADER=testdata/picard/sam/test_cram_file_header_only.cram, testdata/picard/sam/test_cram_file_coordinate_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.062s | passed |
| testShouldWriteCRAMWhenCRAMWithReference[9](picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar, CREATE_INDEX=false, testdata/picard/sam/test_cram_file_query_sorted.cram, testdata/picard/sam/test_cram_file.ref.fa) | 0.377s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[0](picard.sam.AddOrReplaceReadGroups, RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.012s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[10](picard.sam.GatherBamFiles, I=/mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_part_2.cram, testdata/picard/sam/unmapped_part_1.cram) | 0.025s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[11](picard.sam.FastqToSam, F1=testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq.gz SAMPLE_NAME=s1, null) | 0.228s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[12](picard.illumina.IlluminaBasecallsToSam, BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 READ_STRUCTURE=25S8S25T RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=HelloWorld SEQUENCING_CENTER=BI, null) | 0.399s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[13](picard.illumina.MarkIlluminaAdapters, METRICS=/tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters15687353949392762232.txt, testdata/picard/sam/unmapped_queryname_sorted.cram) | 0.020s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[14](picard.sam.SplitSamByLibrary, null, testdata/picard/sam/split_test_unmapped.cram) | 0.039s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[1](picard.sam.CleanSam, null, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.012s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[2](picard.sam.DownsampleSam, null, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.012s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[3](picard.sam.FixMateInformation, null, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.013s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[4](picard.sam.markduplicates.MarkDuplicates, M=/tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicates14136311359580033436.dir, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.800s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[5](picard.sam.MergeSamFiles, null, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.014s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[6](picard.sam.PositionBasedDownsampleSam, FRACTION=0.5, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.008s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[7](picard.sam.SortSam, SORT_ORDER=queryname, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.013s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[8](picard.sam.ReplaceSamHeader, HEADER=testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.cram) | 0.013s | passed |
| testShouldWriteCRAMWhenUnmappedCRAMWithoutReference[9](picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar, CREATE_INDEX=false, testdata/picard/sam/unmapped_with_oq_tag.cram) | 0.023s | passed |
Standard error
[Thu Apr 24 13:03:47 EDT 2025] AddOrReplaceReadGroups --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.AddOrReplaceReadGroups3729299148519030482.cram --RGID 4 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM 20 --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 INFO 2025-04-24 13:03:47 AddOrReplaceReadGroups Created read-group ID=4 PL=illumina LB=lib1 SM=20 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.AddOrReplaceReadGroups3729299148519030482.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.AddOrReplaceReadGroups 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] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.CleanSam15852045699952012219.cram --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.CleanSam15852045699952012219.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.CleanSam 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] DownsampleSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.DownsampleSam8808961384712871773.cram --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 1.0 --ACCURACY 1.0E-4 --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 WARNING 2025-04-24 13:03:47 DownsampleSam Running DownsampleSam with PROBABILITY=1! This will likely just recreate the input file. INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.DownsampleSam8808961384712871773.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.DownsampleSam 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] FixMateInformation --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.FixMateInformation4347159512477317051.cram --ASSUME_SORTED false --ADD_MATE_CIGAR true --IGNORE_MISSING_MATES true --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 INFO 2025-04-24 13:03:47 FixMateInformation Sorting input into queryname order. [Thu Apr 24 13:03:47 EDT 2025] picard.sam.FixMateInformation 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] MarkDuplicates --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicates8285602064458659160.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicates1117559000146991501.dir --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 INFO 2025-04-24 13:03:47 MarkDuplicates Start of doWork freeMemory: 997988200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:47 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:03:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. [Thu Apr 24 13:03:47 EDT 2025] picard.sam.markduplicates.MarkDuplicates 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] MergeSamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.MergeSamFiles5495578347140814195.cram --SORT_ORDER coordinate --ASSUME_SORTED false --MERGE_SEQUENCE_DICTIONARIES false --USE_THREADING 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 INFO 2025-04-24 13:03:47 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.MergeSamFiles5495578347140814195.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.MergeSamFiles 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] PositionBasedDownsampleSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.PositionBasedDownsampleSam17269798303818935563.cram --FRACTION 0.5 --REMOVE_DUPLICATE_INFORMATION true --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS 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 INFO 2025-04-24 13:03:47 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2025-04-24 13:03:47 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. [Thu Apr 24 13:03:47 EDT 2025] picard.sam.PositionBasedDownsampleSam 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] SortSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SortSam2526201614765248106.cram --SORT_ORDER queryname --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SortSam2526201614765248106.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.SortSam 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] ReplaceSamHeader --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --HEADER testdata/picard/sam/test_cram_file_header_only.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.ReplaceSamHeader7897695406403512359.cram --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.ReplaceSamHeader7897695406403512359.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.ReplaceSamHeader 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] RevertOriginalBaseQualitiesAndAddMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar1546920039630966594.cram --RESTORE_ORIGINAL_QUALITIES true --MAX_RECORDS_TO_EXAMINE 10000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX true --CREATE_MD5_FILE true --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.RevertOriginalBaseQualitiesAndAddMateCigar 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] GatherBamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.GatherBamFiles6424082423072779227.cram --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.GatherBamFiles6424082423072779227.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:47 GatherBamFiles Gathering /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram [Thu Apr 24 13:03:47 EDT 2025] picard.sam.GatherBamFiles 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] MarkDuplicatesWithMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicatesWithMateCigar2339932078363027053.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicatesWithMateCigar2726957274460643193.txt --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --BLOCK_SIZE 100000 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicatesWithMateCigar2339932078363027053.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar 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] SimpleMarkDuplicatesWithMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/one_pair_mc.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar4594930624736834239.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/SimpleMarkDuplicatesWithMateCigar8586421587152559285.txt --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar4594930624736834239.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar 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] MarkIlluminaAdapters --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters5482663111556998516.cram --METRICS /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters4745769828291703904.txt --MIN_MATCH_BASES_SE 12 --MIN_MATCH_BASES_PE 6 --MAX_ERROR_RATE_SE 0.1 --MAX_ERROR_RATE_PE 0.1 --ADAPTERS INDEXED --ADAPTERS DUAL_INDEXED --ADAPTERS PAIRED_END --ADAPTER_TRUNCATION_LENGTH 30 --PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN 100 --NUM_ADAPTERS_TO_KEEP 1 --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters5482663111556998516.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.illumina.MarkIlluminaAdapters 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] SplitSamByLibrary --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary16790448261096106815 --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 INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary16790448261096106815/3815246.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary16790448261096106815/g1k-sc-HG00100-A.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:47 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary16790448261096106815/6503965.cram INFO 2025-04-24 13:03:47 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:47 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:47 EDT 2025] picard.sam.SplitSamByLibrary 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] AddOrReplaceReadGroups --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.AddOrReplaceReadGroups6924878221753671541.cram --RGID 4 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM 20 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --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 INFO 2025-04-24 13:03:47 AddOrReplaceReadGroups Created read-group ID=4 PL=illumina LB=lib1 SM=20 [Thu Apr 24 13:03:47 EDT 2025] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:47 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.CleanSam8011468952771946390.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --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.CleanSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:47 EDT 2025] DownsampleSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.DownsampleSam15908356402921646559.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 1.0 --ACCURACY 1.0E-4 --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 WARNING 2025-04-24 13:03:47 DownsampleSam Running DownsampleSam with PROBABILITY=1! This will likely just recreate the input file. INFO 2025-04-24 13:03:47 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:47 DownsampleSam Kept 518 out of 518 reads (100.00%). [Thu Apr 24 13:03:47 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:47 EDT 2025] FixMateInformation --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.FixMateInformation5794661633766208753.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --ASSUME_SORTED false --ADD_MATE_CIGAR true --IGNORE_MISSING_MATES true --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 INFO 2025-04-24 13:03:47 FixMateInformation Sorting input into queryname order. INFO 2025-04-24 13:03:48 FixMateInformation Sorting by queryname complete. INFO 2025-04-24 13:03:48 FixMateInformation Output will be sorted by coordinate INFO 2025-04-24 13:03:48 FixMateInformation Traversing query name sorted records and fixing up mate pair information. INFO 2025-04-24 13:03:48 FixMateInformation Finished processing reads; re-sorting output file. [Thu Apr 24 13:03:48 EDT 2025] picard.sam.FixMateInformation done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:48 EDT 2025] MarkDuplicates --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicates5930386890791990924.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicates15160830643134469511.dir --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 13:03:48 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:48 MarkDuplicates Start of doWork freeMemory: 997942448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:48 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:03:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. WARNING 2025-04-24 13:03:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: ERR013140.3521432. Cause: String 'ERR013140.3521432' did not start with a parsable number. INFO 2025-04-24 13:03:48 MarkDuplicates Read 518 records. 0 pairs never matched. INFO 2025-04-24 13:03:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 934898632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:48 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:03:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:03:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:03:48 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:03:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 996817832; totalMemory: 1610612736; maxMemory: 2147483648 INFO 2025-04-24 13:03:48 MarkDuplicates Marking 22 records as duplicates. INFO 2025-04-24 13:03:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:03:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2025-04-24 13:03:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:03:48 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:03:48 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:03:49 MarkDuplicates Before output close freeMemory: 991680272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:03:49 MarkDuplicates After output close freeMemory: 989236240; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:03:49 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:49 EDT 2025] MergeSamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.MergeSamFiles13070484884487853296.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --SORT_ORDER coordinate --ASSUME_SORTED false --MERGE_SEQUENCE_DICTIONARIES false --USE_THREADING 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 13:03:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:49 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2025-04-24 13:03:49 MergeSamFiles Finished reading inputs. [Thu Apr 24 13:03:49 EDT 2025] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1503657984 [Thu Apr 24 13:03:49 EDT 2025] PositionBasedDownsampleSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.PositionBasedDownsampleSam15368843275266733209.cram --FRACTION 0.5 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --REMOVE_DUPLICATE_INFORMATION true --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS 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 13:03:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:49 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2025-04-24 13:03:49 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2025-04-24 13:03:49 PositionBasedDownsampleSam First pass done. INFO 2025-04-24 13:03:49 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2025-04-24 13:03:49 PositionBasedDownsampleSam Second pass done. WARNING 2025-04-24 13:03:49 PositionBasedDownsampleSam You've requested FRACTION=0.500000, the resulting downsampling resulted in a rate of 0.000000. INFO 2025-04-24 13:03:49 PositionBasedDownsampleSam Finished! Kept 0 out of 518 reads (P=0.00000). [Thu Apr 24 13:03:49 EDT 2025] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1503657984 [Thu Apr 24 13:03:49 EDT 2025] SortSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SortSam8029233679145583543.cram --SORT_ORDER queryname --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --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 13:03:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:49 SortSam Finished reading inputs, merging and writing to output now. [Thu Apr 24 13:03:49 EDT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:49 EDT 2025] ReplaceSamHeader --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --HEADER testdata/picard/sam/test_cram_file_header_only.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.ReplaceSamHeader8298590828098090206.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --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 13:03:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:03:49 EDT 2025] picard.sam.ReplaceSamHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:49 EDT 2025] RevertOriginalBaseQualitiesAndAddMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar853228199566265075.cram --CREATE_INDEX false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --RESTORE_ORIGINAL_QUALITIES true --MAX_RECORDS_TO_EXAMINE 10000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE true --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:49 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:49 RevertOriginalBaseQualitiesAndAddMateCigar Cannot skip the SAM/BAM/CRAM as we found a mate with no mate cigar tag INFO 2025-04-24 13:03:49 RevertOriginalBaseQualitiesAndAddMateCigar Reverted the original base qualities for 0 records INFO 2025-04-24 13:03:50 RevertOriginalBaseQualitiesAndAddMateCigar Updated 518 records with mate cigar [Thu Apr 24 13:03:50 EDT 2025] picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] GatherBamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.GatherBamFiles767376196672944933.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 GatherBamFiles Gathering /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram INFO 2025-04-24 13:03:50 GatherBamFiles Gathering /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram [Thu Apr 24 13:03:50 EDT 2025] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] MarkDuplicatesWithMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicatesWithMateCigar4294225370999811730.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicatesWithMateCigar847294910959987490.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --MINIMUM_DISTANCE -1 --SKIP_PAIRS_WITH_NO_MATE_CIGAR true --BLOCK_SIZE 100000 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: ERR013140.23480670. Cause: String 'ERR013140.23480670' did not start with a parsable number. WARNING 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: ERR013140.3521432 1/2 108b aligned to 17:1-86. INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Processed 518 records INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Found 517 records with no mate cigar optional tag. INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. [Thu Apr 24 13:03:50 EDT 2025] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/MarkDuplicates/one_pair_mc.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar753580209564008594.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/SimpleMarkDuplicatesWithMateCigar10811745762715745254.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: ERR013140.3521432. Cause: String 'ERR013140.3521432' did not start with a parsable number. INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:03:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:03:50 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] ReorderSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.ReorderSam1056085155617107002.cram --SEQUENCE_DICTIONARY testdata/picard/sam/test_cram_file.ref.fa --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 ReorderSam SAM/BAM/CRAM file INFO 2025-04-24 13:03:50 ReorderSam SN=17 LN=4200 INFO 2025-04-24 13:03:50 ReorderSam Reference INFO 2025-04-24 13:03:50 ReorderSam SN=17 LN=4200 INFO 2025-04-24 13:03:50 ReorderSam Reordering SAM/BAM/CRAM file: INFO 2025-04-24 13:03:50 ReorderSam Reordering read contig 17 [index=0] to => ref contig 17 [index=0] INFO 2025-04-24 13:03:50 ReorderSam Writing reads... INFO 2025-04-24 13:03:50 ReorderSam writing the reads from 17 INFO 2025-04-24 13:03:50 ReorderSam Processing 17 INFO 2025-04-24 13:03:50 ReorderSam Wrote 518 reads INFO 2025-04-24 13:03:50 ReorderSam Processing unmapped INFO 2025-04-24 13:03:50 ReorderSam Wrote 0 reads [Thu Apr 24 13:03:50 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] SetNmMdAndUqTags --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SetNmMdAndUqTags8820117573400920909.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --IS_BISULFITE_SEQUENCE false --SET_ONLY_UQ 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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:03:50 EDT 2025] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.cram --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.MergeBamAlignment5353892867172222622.cram --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.cram] WARNING 2025-04-24 13:03:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC WARNING 2025-04-24 13:03:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC INFO 2025-04-24 13:03:50 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. [Thu Apr 24 13:03:50 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] MarkIlluminaAdapters --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_query_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters12252871168027179716.cram --METRICS /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters14016845742977392570.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --MIN_MATCH_BASES_SE 12 --MIN_MATCH_BASES_PE 6 --MAX_ERROR_RATE_SE 0.1 --MAX_ERROR_RATE_PE 0.1 --ADAPTERS INDEXED --ADAPTERS DUAL_INDEXED --ADAPTERS PAIRED_END --ADAPTER_TRUNCATION_LENGTH 30 --PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN 100 --NUM_ADAPTERS_TO_KEEP 1 --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:03:50 EDT 2025] picard.illumina.MarkIlluminaAdapters done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] SplitSamByLibrary --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file_coordinate_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary7550033410642741575 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/test_cram_file.ref.fa --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 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 13:03:50 EDT 2025] picard.sam.SplitSamByLibrary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] AddOrReplaceReadGroups --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.AddOrReplaceReadGroups12771062083636070065.cram --RGID 4 --RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM 20 --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 AddOrReplaceReadGroups Created read-group ID=4 PL=illumina LB=lib1 SM=20 INFO 2025-04-24 13:03:50 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.AddOrReplaceReadGroups12771062083636070065.cram INFO 2025-04-24 13:03:50 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:50 EDT 2025] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.CleanSam8901161875676980370.cram --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.CleanSam8901161875676980370.cram INFO 2025-04-24 13:03:50 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:50 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] DownsampleSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.DownsampleSam11484152319511685477.cram --STRATEGY ConstantMemory --RANDOM_SEED 1 --PROBABILITY 1.0 --ACCURACY 1.0E-4 --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:50 DownsampleSam Running DownsampleSam with PROBABILITY=1! This will likely just recreate the input file. INFO 2025-04-24 13:03:50 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.DownsampleSam11484152319511685477.cram INFO 2025-04-24 13:03:50 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:50 DownsampleSam Finished downsampling. INFO 2025-04-24 13:03:50 DownsampleSam Kept 12 out of 12 reads (100.00%). [Thu Apr 24 13:03:50 EDT 2025] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] FixMateInformation --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.FixMateInformation16382109431039455633.cram --ASSUME_SORTED false --ADD_MATE_CIGAR true --IGNORE_MISSING_MATES true --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 FixMateInformation Output will be sorted by queryname INFO 2025-04-24 13:03:50 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.FixMateInformation16382109431039455633.cram INFO 2025-04-24 13:03:50 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:50 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:50 FixMateInformation Traversing query name sorted records and fixing up mate pair information. INFO 2025-04-24 13:03:50 FixMateInformation Closing output file. [Thu Apr 24 13:03:50 EDT 2025] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:50 EDT 2025] MarkDuplicates --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicates9616606105514097575.cram --METRICS_FILE /tmp/CramCompatibilityTest.tmp4125272008596007021/MarkDuplicates14136311359580033436.dir --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --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 13:03:50 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:50 MarkDuplicates Start of doWork freeMemory: 997944008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:50 MarkDuplicates Reading input file and constructing read end information. INFO 2025-04-24 13:03:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2025-04-24 13:03:50 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2025-04-24 13:03:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 935025752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:50 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2025-04-24 13:03:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2025-04-24 13:03:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2025-04-24 13:03:51 MarkDuplicates Sorting list of duplicate records. INFO 2025-04-24 13:03:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 889936864; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2025-04-24 13:03:51 MarkDuplicates Marking 0 records as duplicates. INFO 2025-04-24 13:03:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2025-04-24 13:03:51 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.markduplicates.MarkDuplicates9616606105514097575.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2025-04-24 13:03:51 MarkDuplicates Duplicate Index cleanup. INFO 2025-04-24 13:03:51 MarkDuplicates Getting Memory Stats. INFO 2025-04-24 13:03:51 MarkDuplicates Before output close freeMemory: 992443800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2025-04-24 13:03:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2025-04-24 13:03:51 MarkDuplicates After output close freeMemory: 989558832; totalMemory: 1073741824; maxMemory: 2147483648 [Thu Apr 24 13:03:51 EDT 2025] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] MergeSamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.MergeSamFiles5818416786211729382.cram --SORT_ORDER coordinate --ASSUME_SORTED false --MERGE_SEQUENCE_DICTIONARIES false --USE_THREADING 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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 MergeSamFiles Sorting input files using temp directory [/tmp/root] INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.MergeSamFiles5818416786211729382.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 MergeSamFiles Finished reading inputs. [Thu Apr 24 13:03:51 EDT 2025] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] PositionBasedDownsampleSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.PositionBasedDownsampleSam3555674996193793000.cram --FRACTION 0.5 --REMOVE_DUPLICATE_INFORMATION true --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS 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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2025-04-24 13:03:51 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2025-04-24 13:03:51 PositionBasedDownsampleSam First pass done. INFO 2025-04-24 13:03:51 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.PositionBasedDownsampleSam3555674996193793000.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 PositionBasedDownsampleSam Second pass done. WARNING 2025-04-24 13:03:51 PositionBasedDownsampleSam You've requested FRACTION=0.500000, the resulting downsampling resulted in a rate of 0.000000. INFO 2025-04-24 13:03:51 PositionBasedDownsampleSam Finished! Kept 0 out of 12 reads (P=0.00000). [Thu Apr 24 13:03:51 EDT 2025] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] SortSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SortSam1717278562356888309.cram --SORT_ORDER queryname --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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SortSam1717278562356888309.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 SortSam Finished reading inputs, merging and writing to output now. [Thu Apr 24 13:03:51 EDT 2025] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] ReplaceSamHeader --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/SamFormatConverterTest/unmapped.cram --HEADER testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.ReplaceSamHeader12274868081461858358.cram --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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.ReplaceSamHeader12274868081461858358.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:51 EDT 2025] picard.sam.ReplaceSamHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] RevertOriginalBaseQualitiesAndAddMateCigar --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_with_oq_tag.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar12359005286552184784.cram --CREATE_INDEX false --RESTORE_ORIGINAL_QUALITIES true --MAX_RECORDS_TO_EXAMINE 10000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_MD5_FILE true --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC INFO 2025-04-24 13:03:51 RevertOriginalBaseQualitiesAndAddMateCigar Cannot skip the SAM/BAM/CRAM as we found a record with an OQ INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar12359005286552184784.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC INFO 2025-04-24 13:03:51 RevertOriginalBaseQualitiesAndAddMateCigar Reverted the original base qualities for 4 records INFO 2025-04-24 13:03:51 RevertOriginalBaseQualitiesAndAddMateCigar Updated 4 records with mate cigar INFO 2025-04-24 13:03:51 RevertOriginalBaseQualitiesAndAddMateCigar Did not find any paired mapped reads. [Thu Apr 24 13:03:51 EDT 2025] picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] GatherBamFiles --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_part_1.cram --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_part_2.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.GatherBamFiles12780706443381548423.cram --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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.GatherBamFiles12780706443381548423.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 GatherBamFiles Gathering /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_part_1.cram WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC INFO 2025-04-24 13:03:51 GatherBamFiles Gathering /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_part_2.cram WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC [Thu Apr 24 13:03:51 EDT 2025] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] FastqToSam --FASTQ testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq.gz --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.FastqToSam7432211266763887771.cram --SAMPLE_NAME s1 --USE_SEQUENTIAL_FASTQS false --READ_GROUP_NAME A --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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.FastqToSam7432211266763887771.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 FastqToSam Auto-detected quality format as: Standard. INFO 2025-04-24 13:03:51 FastqToSam Processed 5000 fastq reads [Thu Apr 24 13:03:51 EDT 2025] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:51 EDT 2025] IlluminaBasecallsToSam --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.IlluminaBasecallsToSam9772148245669886743.cram --RUN_BARCODE HiMom --SAMPLE_ALIAS HiDad --LIBRARY_NAME HelloWorld --SEQUENCING_CENTER BI --LANE 1 --READ_STRUCTURE 25S8S25T --BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls --PLATFORM ILLUMINA --INCLUDE_BC_IN_RG_TAG false --ADAPTERS_TO_CHECK INDEXED --ADAPTERS_TO_CHECK DUAL_INDEXED --ADAPTERS_TO_CHECK NEXTERA_V2 --ADAPTERS_TO_CHECK FLUIDIGM --NUM_PROCESSORS 0 --APPLY_EAMSS_FILTER true --MAX_READS_IN_RAM_PER_TILE -1 --INCLUDE_NON_PF_READS true --IGNORE_UNEXPECTED_BARCODES false --MOLECULAR_INDEX_TAG RX --MOLECULAR_INDEX_BASE_QUALITY_TAG QX --BARCODE_POPULATION_STRATEGY ORPHANS_ONLY --INCLUDE_BARCODE_QUALITY false --SORT true --MATCH_BARCODES_INLINE false --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS 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 13:03:51 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.IlluminaBasecallsToSam9772148245669886743.cram INFO 2025-04-24 13:03:51 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:51 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:51 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T INFO 2025-04-24 13:03:51 SortedBasecallsConverter Tile Read Executor - Queueing: 3 TileProcessor jobs INFO 2025-04-24 13:03:51 SortedBasecallsConverter Done with awaitExecutor: Tile Read Executor INFO 2025-04-24 13:03:51 SortedBasecallsConverter Tile 1101 Writer Executor Starting INFO 2025-04-24 13:03:51 SortedBasecallsConverter Done with awaitExecutor: Tile 1101 Writer Executor INFO 2025-04-24 13:03:51 SortedBasecallsConverter Tile 1201 Writer Executor Starting INFO 2025-04-24 13:03:52 SortedBasecallsConverter Done with awaitExecutor: Tile 1201 Writer Executor INFO 2025-04-24 13:03:52 SortedBasecallsConverter Tile 2101 Writer Executor Starting INFO 2025-04-24 13:03:52 SortedBasecallsConverter Done with awaitExecutor: Tile 2101 Writer Executor [Thu Apr 24 13:03:52 EDT 2025] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:52 EDT 2025] MarkIlluminaAdapters --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped_queryname_sorted.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters18075970315061688268.cram --METRICS /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters15687353949392762232.txt --MIN_MATCH_BASES_SE 12 --MIN_MATCH_BASES_PE 6 --MAX_ERROR_RATE_SE 0.1 --MAX_ERROR_RATE_PE 0.1 --ADAPTERS INDEXED --ADAPTERS DUAL_INDEXED --ADAPTERS PAIRED_END --ADAPTER_TRUNCATION_LENGTH 30 --PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN 100 --NUM_ADAPTERS_TO_KEEP 1 --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 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:52 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.illumina.MarkIlluminaAdapters18075970315061688268.cram INFO 2025-04-24 13:03:52 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:52 EDT 2025] picard.illumina.MarkIlluminaAdapters done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:03:52 EDT 2025] SplitSamByLibrary --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/split_test_unmapped.cram --OUTPUT /tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary7824266577850482148 --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 13:03:52 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:03:52 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary7824266577850482148/lib-3.cram INFO 2025-04-24 13:03:52 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false INFO 2025-04-24 13:03:52 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary7824266577850482148/lib-1.cram INFO 2025-04-24 13:03:52 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false WARNING 2025-04-24 13:03:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN WARNING 2025-04-24 13:03:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC INFO 2025-04-24 13:03:52 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/CramCompatibilityTest.tmp4125272008596007021/picard.sam.SplitSamByLibrary7824266577850482148/unknown.cram INFO 2025-04-24 13:03:52 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2025-04-24 13:03:52 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false [Thu Apr 24 13:03:52 EDT 2025] picard.sam.SplitSamByLibrary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824