| 20260507 17:52:06.678 | INFO | Snapshot : (Legend) % CPU / Threads / ResMem GiB | 20260507 17:52:06.678 | INFO | Snapshot : 0.0% / 3T / 0.0G | 20260507 17:52:06.679 | INFO | Effective command line: /opt/pacbio/bin/baz2bam --splitControlRefLength=15000 --platform=REVIO --splitControlLength=10000 --stemLength=8 --minSubLength=100 --minHardAccuracy=-1 --minZmwLength=1 --process-log-interval=5000 --metadata=/data/icc/m84031_260507_084733_s1/metadata/m84031_260507_084733_s1_basic_preview_4hr.metadata.xml --defaultZmwBatchSize=75 --maxInputQueueMB=3500 --flankLength=-1 --fileListStride=1 --statusfd=2 --startFileListIdx=0 --nProcs=24 --minSoftAccuracy=-1 --minFlankingScore=-1 --bamThreads=8 --minEmptyTime=60 --output=m84031_260507_084733_s1_basic_preview_4hr --minInsertionLength=50 --bazThreads=2 --instrument-files-layout --maxNumZmwsToProcess=2147483647 --smrtMaskScoreThreshold=-1 --streamedBam --zmwOutputStride=0 --minSnr=0 --hqrfConfig=DEFAULT --process-log=NONE --emptyOutlierTime=3 --inlinePbi --whitelistZmwNum=0 --uuid=04d94881-c0b0-44d5-b283-f635fa67ab6f --silent --whitelistZmwId=0 --samplePercent=100 --zmwBatchMB=250 --zmwHeaderBatchMB=10 --maxOutputQueueMB=5000 --log-level=INFO --log-file=/data/icc/m84031_260507_084733_s1/metadata/m84031_260507_084733_s1_basic_preview_4hr.baz2bam.log /data/nrta/2/m84031_260507_084733_s1/pb_internal/baz/m84031_260507_084733_s1_basic_preview.baz | 20260507 17:52:06.679 | INFO | Start | 20260507 17:52:06.679 | INFO | /opt/pacbio/bin/baz2bam --splitControlRefLength=15000 --platform=REVIO --splitControlLength=10000 --stemLength=8 --minSubLength=100 --minHardAccuracy=-1 --minZmwLength=1 --process-log-interval=5000 --metadata=/data/icc/m84031_260507_084733_s1/metadata/m84031_260507_084733_s1_basic_preview_4hr.metadata.xml --defaultZmwBatchSize=75 --maxInputQueueMB=3500 --flankLength=-1 --fileListStride=1 --statusfd=2 --startFileListIdx=0 --nProcs=24 --minSoftAccuracy=-1 --minFlankingScore=-1 --bamThreads=8 --minEmptyTime=60 --output=m84031_260507_084733_s1_basic_preview_4hr --minInsertionLength=50 --bazThreads=2 --instrument-files-layout --maxNumZmwsToProcess=2147483647 --smrtMaskScoreThreshold=-1 --streamedBam --zmwOutputStride=0 --minSnr=0 --hqrfConfig=DEFAULT --process-log=NONE --emptyOutlierTime=3 --inlinePbi --whitelistZmwNum=0 --uuid=04d94881-c0b0-44d5-b283-f635fa67ab6f --silent --whitelistZmwId=0 --samplePercent=100 --zmwBatchMB=250 --zmwHeaderBatchMB=10 --maxOutputQueueMB=5000 --log-level=INFO --log-file=/data/icc/m84031_260507_084733_s1/metadata/m84031_260507_084733_s1_basic_preview_4hr.baz2bam.log /data/nrta/2/m84031_260507_084733_s1/pb_internal/baz/m84031_260507_084733_s1_basic_preview.baz | 20260507 17:52:06.679 | INFO | commit hash: 2dc54f5a66f39b94662202d5514157d553e25f7d | 20260507 17:52:06.679 | INFO | commit date: 2026-01-13 11:49:20 +0100 | 20260507 17:52:06.679 | INFO | Version: release/kestrel-13.5_2dc54f5a66f39b94662202d5514157d553e25f7d | 20260507 17:52:06.679 | INFO | Roughly processing the first 2147483647 ZMWs, up to a slice boundary... | 20260507 17:52:07.007 | INFO | Parsing "/data/icc/m84031_260507_084733_s1/metadata/m84031_260507_084733_s1_basic_preview_4hr.metadata.xml" | 20260507 17:52:07.009 | INFO | PPAAlgoConfig = {"adapterFinding":{"disableAdapterFinding":false,"leftAdapter":"CAACAACAACAACGGAGGAGGAGGAAAAG","rightAdapter":"CAACAACAACAACGGAGGAGGAGGAAAAG"},"controlFilter":{"disableControlFiltering":false,"leftAdapter":"TAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA","rightAdapter":"TAGAGAGAGAAAAGGAGGAGGAGGCAACAACAACAACTCTCTCTA","sequence":"TCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTGGCCGCATCCAGACTCAAATCAACGACCAGATCGCCTACCGGTTCAGCCATACCGGACTCCTCCTGCGATCCCTTCTGATACTGTCATCAGCATTACGTCATCCTCCGTCATGTCCGCCACATCCGGGGAAGCGGGGATAACTTCATTCCCGTCCGGGCCAAAGCGGACACCTCCGGCAAGCCCTGCCGCTTTCTGCAGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTCAGATCAAAAATAGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTA"},"hqrf":{"method":"N2"},"inputFilter":{"minSnr":1.5},"outputFilter":{"zmwOutputStride":1}} | 20260507 17:52:07.471 | INFO | 24 adapter callers have been configured with the standard method | 20260507 17:52:07.472 | INFO | Created BAM Header comment:{ "collection_metadata_xml" : "", "dataset_uuid" : "bde72dbe-e759-4303-9af8-efb1e65544fb", "external_resources" : [ { "file_name" : "../metadata/m84031_260507_084733_s1_basic_preview_4hr.sts.xml", "meta_type" : "PacBio.SubreadFile.ChipStatsFile" } ], "name" : "baz2bam_ccs_sideband", "subreadset_name" : "Acq15-Cell1", "version" : "1.2", "zmws" : 24576 } | 20260507 17:52:07.472 | INFO | bam file: - | 20260507 17:52:07.472 | INFO | bamThreads = 8 | 20260507 17:52:07.472 | INFO | Writing streaming BAM file to stdout | 20260507 17:52:07.483 | INFO | ZOFFSET_CART_HMM configured | 20260507 17:52:07.483 | INFO | Creating sts.h5 file "pb_internal/m84031_260507_084733_s1_basic_preview_4hr.sts.h5" with parameters numHoles:24576 numAnalogs:4 numFilters:1 | 20260507 17:52:07.486 | INFO | Starting Baz2bam. MovieName: /data/nrta/2/m84031_260507_084733_s1/pb_internal/baz/m84031_260507_084733_s1_basic_preview.baz, BaseCallerVersion: 5.0.0, BazWriterVersion: 0.0.0, BazVersion: 2.6.2, OutputPrefix: "m84031_260507_084733_s1_basic_preview_4hr", ProdFileLayout: Kestrel, Baz2bamVersion: release/kestrel-13.5_2dc54f5a66f39b94662202d5514157d553e25f7d | 20260507 17:52:07.486 | INFO | Spawn 24 workers | 20260507 17:52:07.730 | INFO | Beginning read of next slice | 20260507 17:52:07.730 | INFO | OOM score went from -1 to 1268 | 20260507 17:52:08.730 | INFO | OOM score went from 1268 to 1270 | 20260507 17:52:08.991 | INFO | Finished read of next slice | 20260507 17:52:08.991 | WARN | Anomalous profiling event (reported in ms): | 20260507 17:52:08.991 | WARN | READ_PROFILES measured slower than specified threshold of 3.40282e+38 standard deviations | 20260507 17:52:08.991 | WARN | IDs: Historic mean +- stdev, [ Current Measurements ] | 20260507 17:52:08.991 | WARN | ---------------------------------------------------------- | 20260507 17:52:08.991 | WARN | Full: 0.00e+00 +- 0.00e+00, [ 1.26e+03 ] | 20260507 17:52:08.991 | WARN | TOTAL: 1.95e-03 +- 0.00e+00, [ 1.95e-03 ] | 20260507 17:52:08.991 | WARN | READ_DATA: 1.26e+03 +- 0.00e+00, [ 1.26e+03 ] | 20260507 17:52:08.991 | WARN | SEND_DATA: 2.69e-01 +- 0.00e+00, [ 2.69e-01 ] | 20260507 17:52:08.991 | INFO | Beginning read of next slice | 20260507 17:52:09.730 | INFO | OOM score went from 1270 to 1271 | 20260507 17:52:09.730 | INFO | Sending progress 0.100707 | 20260507 17:52:10.733 | INFO | Sending progress 0.283811 | 20260507 17:52:11.679 | INFO | Snapshot : 620.8% / 40T / 2.2G | 20260507 17:52:11.727 | INFO | Finished read of next slice | 20260507 17:52:11.727 | WARN | Anomalous profiling event (reported in ms): | 20260507 17:52:11.727 | WARN | READ_PROFILES measured slower than specified threshold of 3.40282e+38 standard deviations | 20260507 17:52:11.727 | WARN | IDs: Historic mean +- stdev, [ Current Measurements ] | 20260507 17:52:11.727 | WARN | ---------------------------------------------------------- | 20260507 17:52:11.727 | WARN | Full: 1.26e+03 +- 0.00e+00, [ 2.74e+03 ] | 20260507 17:52:11.727 | WARN | TOTAL: 1.71e-03 +- 3.45e-04, [ 1.46e-03 ] | 20260507 17:52:11.727 | WARN | READ_DATA: 2.00e+03 +- 1.04e+03, [ 2.74e+03 ] | 20260507 17:52:11.727 | WARN | SEND_DATA: 2.77e-01 +- 1.11e-02, [ 2.85e-01 ] | 20260507 17:52:11.727 | INFO | Beginning read of next slice | 20260507 17:52:11.743 | INFO | Sending progress 0.371700 | 20260507 17:52:12.416 | INFO | Finished read of next slice | 20260507 17:52:12.419 | INFO | Final Performance Profiling Results for READ_PROFILES: (reported in milliseconds) | 20260507 17:52:12.419 | INFO | PerfReport: Gathered 3 samples. | 20260507 17:52:12.419 | INFO | PerfReport: % Compute, FullMean/OutlierMean FullDev/OutlierDev | 20260507 17:52:12.419 | INFO | PerfReport: Full Execution -- 1.56e+03 / 2.00e+03, 1.06e+03 / 1.04e+03 | 20260507 17:52:12.419 | INFO | PerfReport: 0.00%, TOTAL -- 1.22e-03 / 1.71e-03, 8.80e-04 / 3.45e-04 | 20260507 17:52:12.419 | INFO | PerfReport: 99.98%, READ_DATA -- 1.56e+03 / 2.00e+03, 1.06e+03 / 1.04e+03 | 20260507 17:52:12.419 | INFO | PerfReport: 0.02%, SEND_DATA -- 2.82e-01 / 2.77e-01, 1.12e-02 / 1.11e-02 | 20260507 17:52:12.743 | INFO | Sending progress 0.615839 | 20260507 17:52:13.747 | INFO | Sending progress 0.798942 | 20260507 17:52:14.596 | INFO | Closing BAM files | 20260507 17:52:14.596 | INFO | Writing PBI files | 20260507 17:52:14.757 | INFO | Sending progress 0.999990 | 20260507 17:52:15.596 | INFO | Corrected missing adapter (>35% per ZMW) in 9 ZMWs, 0.146891% of 6127 total ZMWs with adapters | 20260507 17:52:15.596 | INFO | Corrected missed adapter (<=35% per ZMW) in 34 ZMWs, 0.554921% of 6127 total ZMWs with adapters | 20260507 17:52:15.596 | INFO | Corrected adapters in 43 ZMWs, 0.701812% of 6127 total ZMWs with adapters | 20260507 17:52:15.596 | INFO | Adapter Correction imputed 58 of 9263 total adapters (0.626147%) | 20260507 17:52:15.596 | INFO | Opening file "metadata/m84031_260507_084733_s1_basic_preview_4hr.sts.xml.tmp" | 20260507 17:52:15.640 | INFO | Renaming file "metadata/m84031_260507_084733_s1_basic_preview_4hr.sts.xml.tmp" -> "metadata/m84031_260507_084733_s1_basic_preview_4hr.sts.xml" | 20260507 17:52:15.650 | INFO | BAM files closed and PBIs written | 20260507 17:52:15.650 | INFO | Closing sts.h5 file | 20260507 17:52:15.652 | INFO | sts.h5 file closed and written | 20260507 17:52:15.652 | INFO | Finished ZMW processing 24576 | 20260507 17:52:15.653 | INFO | Finished | 20260507 17:52:15.653 | INFO | Final Performance Profiling Results for COMPUTE_PROFILES: (reported in milliseconds) | 20260507 17:52:15.653 | INFO | PerfReport: Gathered 5354 samples. | 20260507 17:52:15.653 | INFO | PerfReport: % Compute, FullMean/OutlierMean FullDev/OutlierDev | 20260507 17:52:15.653 | INFO | PerfReport: Full Execution -- 3.08e+01 / 3.29e+02, 8.82e+01 / 5.74e+00 | 20260507 17:52:15.653 | INFO | PerfReport: 31.28%, DATA_WAIT -- 9.64e+00 / 2.95e-01, 2.33e+00 / 3.92e-03 | 20260507 17:52:15.653 | INFO | PerfReport: 0.07%, DATA_MOVE -- 3.56e-01 / 3.38e-01, 1.28e+00 / 7.25e-03 | 20260507 17:52:15.653 | INFO | PerfReport: 0.00%, DATA_SEND -- 1.69e-02 / 1.44e-02, 4.73e-03 / 7.44e-04 | 20260507 17:52:15.653 | INFO | PerfReport: 10.22%, PARSE_BINARY -- 6.86e-01 / 7.50e-01, 2.16e+00 / 2.04e+00 | 20260507 17:52:15.653 | INFO | PerfReport: 4.49%, PROCESS_PACKETS -- 3.02e-01 / 2.22e-01, 1.90e+00 / 8.41e-01 | 20260507 17:52:15.653 | INFO | PerfReport: 5.22%, FIND_HQRF -- 3.51e-01 / 3.88e-01, 5.76e-01 / 5.31e-01 | 20260507 17:52:15.653 | INFO | PerfReport: 8.06%, FIND_INSERTS -- 5.41e-01 / 4.09e-01, 2.65e+00 / 8.91e-01 | 20260507 17:52:15.653 | INFO | PerfReport: 0.03%, PROD_STATS -- 2.13e-03 / 2.58e-03, 2.93e-02 / 1.24e-02 | 20260507 17:52:15.653 | INFO | PerfReport: 34.06%, FIND_SUBREAD -- 2.29e+00 / 2.15e+00, 5.66e+00 / 4.16e+00 | 20260507 17:52:15.653 | INFO | PerfReport: 5.21%, ZMW_STATS -- 3.50e-01 / 3.79e-01, 7.16e-01 / 7.09e-01 | 20260507 17:52:15.653 | INFO | PerfReport: 1.34%, FINALIZE -- 9.02e-02 / 7.47e-02, 1.10e+00 / 4.91e-01 | 20260507 17:52:15.653 | INFO | joining thread pool | 20260507 17:52:15.653 | INFO | joining loggingThread_ | 20260507 17:52:15.769 | INFO | joining done | 20260507 17:52:15.769 | INFO | ~ConvertBaz2BamDestroyed | 20260507 17:52:15.769 | INFO | Remap Stats: shiftedHqRegionStart = 12302 noStartOnLabelTransition = 0 noEndOnLabelTransition = 0 | 20260507 17:52:15.956 | INFO | Run Time : 9s 277ms | 20260507 17:52:15.956 | INFO | CPU Time : 1m 17s | 20260507 17:52:15.956 | INFO | Peak RSS : 2.826 GB | 20260507 17:52:15.956 | INFO | Exit code : 0