| 20260505 07:31:28.706 | INFO | Snapshot : (Legend) % CPU / Threads / ResMem GiB | 20260505 07:31:28.707 | INFO | Snapshot : 0.0% / 3T / 0.0G | 20260505 07:31:28.707 | 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_260504_231011_s1/metadata/m84031_260504_231011_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_260504_231011_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=c2d51006-4171-4f34-9965-e8acec170309 --silent --whitelistZmwId=0 --samplePercent=100 --zmwBatchMB=250 --zmwHeaderBatchMB=10 --maxOutputQueueMB=5000 --log-level=INFO --log-file=/data/icc/m84031_260504_231011_s1/metadata/m84031_260504_231011_s1_basic_preview_4hr.baz2bam.log /data/nrta/2/m84031_260504_231011_s1/pb_internal/baz/m84031_260504_231011_s1_basic_preview.baz | 20260505 07:31:28.707 | INFO | Start | 20260505 07:31:28.707 | 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_260504_231011_s1/metadata/m84031_260504_231011_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_260504_231011_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=c2d51006-4171-4f34-9965-e8acec170309 --silent --whitelistZmwId=0 --samplePercent=100 --zmwBatchMB=250 --zmwHeaderBatchMB=10 --maxOutputQueueMB=5000 --log-level=INFO --log-file=/data/icc/m84031_260504_231011_s1/metadata/m84031_260504_231011_s1_basic_preview_4hr.baz2bam.log /data/nrta/2/m84031_260504_231011_s1/pb_internal/baz/m84031_260504_231011_s1_basic_preview.baz | 20260505 07:31:28.707 | INFO | commit hash: 2dc54f5a66f39b94662202d5514157d553e25f7d | 20260505 07:31:28.707 | INFO | commit date: 2026-01-13 11:49:20 +0100 | 20260505 07:31:28.707 | INFO | Version: release/kestrel-13.5_2dc54f5a66f39b94662202d5514157d553e25f7d | 20260505 07:31:28.707 | INFO | Roughly processing the first 2147483647 ZMWs, up to a slice boundary... | 20260505 07:31:28.999 | INFO | Parsing "/data/icc/m84031_260504_231011_s1/metadata/m84031_260504_231011_s1_basic_preview_4hr.metadata.xml" | 20260505 07:31:29.001 | 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}} | 20260505 07:31:29.358 | INFO | 24 adapter callers have been configured with the standard method | 20260505 07:31:29.360 | INFO | Created BAM Header comment:{ "collection_metadata_xml" : "", "dataset_uuid" : "3bd380ef-b6bc-4bc7-87c9-819f8c0fc430", "external_resources" : [ { "file_name" : "../metadata/m84031_260504_231011_s1_basic_preview_4hr.sts.xml", "meta_type" : "PacBio.SubreadFile.ChipStatsFile" } ], "name" : "baz2bam_ccs_sideband", "subreadset_name" : "Acq13-Cell1", "version" : "1.2", "zmws" : 24576 } | 20260505 07:31:29.360 | INFO | bam file: - | 20260505 07:31:29.360 | INFO | bamThreads = 8 | 20260505 07:31:29.360 | INFO | Writing streaming BAM file to stdout | 20260505 07:31:29.371 | INFO | ZOFFSET_CART_HMM configured | 20260505 07:31:29.371 | INFO | Creating sts.h5 file "pb_internal/m84031_260504_231011_s1_basic_preview_4hr.sts.h5" with parameters numHoles:24576 numAnalogs:4 numFilters:1 | 20260505 07:31:29.374 | INFO | Starting Baz2bam. MovieName: /data/nrta/2/m84031_260504_231011_s1/pb_internal/baz/m84031_260504_231011_s1_basic_preview.baz, BaseCallerVersion: 5.0.0, BazWriterVersion: 0.0.0, BazVersion: 2.6.2, OutputPrefix: "m84031_260504_231011_s1_basic_preview_4hr", ProdFileLayout: Kestrel, Baz2bamVersion: release/kestrel-13.5_2dc54f5a66f39b94662202d5514157d553e25f7d | 20260505 07:31:29.374 | INFO | Spawn 24 workers | 20260505 07:31:29.617 | INFO | Beginning read of next slice | 20260505 07:31:29.617 | INFO | OOM score went from -1 to 1268 | 20260505 07:31:30.617 | INFO | OOM score went from 1268 to 1270 | 20260505 07:31:30.796 | INFO | Finished read of next slice | 20260505 07:31:30.797 | WARN | Anomalous profiling event (reported in ms): | 20260505 07:31:30.797 | WARN | READ_PROFILES measured slower than specified threshold of 3.40282e+38 standard deviations | 20260505 07:31:30.797 | WARN | IDs: Historic mean +- stdev, [ Current Measurements ] | 20260505 07:31:30.797 | WARN | ---------------------------------------------------------- | 20260505 07:31:30.797 | WARN | Full: 0.00e+00 +- 0.00e+00, [ 1.18e+03 ] | 20260505 07:31:30.797 | WARN | TOTAL: 9.77e-04 +- 0.00e+00, [ 9.77e-04 ] | 20260505 07:31:30.797 | WARN | READ_DATA: 1.18e+03 +- 0.00e+00, [ 1.18e+03 ] | 20260505 07:31:30.797 | WARN | SEND_DATA: 2.08e-01 +- 0.00e+00, [ 2.08e-01 ] | 20260505 07:31:30.797 | INFO | Beginning read of next slice | 20260505 07:31:31.617 | INFO | OOM score went from 1270 to 1271 | 20260505 07:31:31.617 | INFO | Sending progress 0.128173 | 20260505 07:31:32.618 | INFO | Sending progress 0.307411 | 20260505 07:31:32.931 | INFO | Finished read of next slice | 20260505 07:31:32.932 | WARN | Anomalous profiling event (reported in ms): | 20260505 07:31:32.932 | WARN | READ_PROFILES measured slower than specified threshold of 3.40282e+38 standard deviations | 20260505 07:31:32.932 | WARN | IDs: Historic mean +- stdev, [ Current Measurements ] | 20260505 07:31:32.932 | WARN | ---------------------------------------------------------- | 20260505 07:31:32.932 | WARN | Full: 1.18e+03 +- 0.00e+00, [ 2.13e+03 ] | 20260505 07:31:32.932 | WARN | TOTAL: 4.88e-04 +- 6.91e-04, [ 0.00e+00 ] | 20260505 07:31:32.932 | WARN | READ_DATA: 1.66e+03 +- 6.76e+02, [ 2.13e+03 ] | 20260505 07:31:32.932 | WARN | SEND_DATA: 2.31e-01 +- 3.25e-02, [ 2.54e-01 ] | 20260505 07:31:32.932 | INFO | Beginning read of next slice | 20260505 07:31:33.623 | INFO | Sending progress 0.438635 | 20260505 07:31:33.718 | INFO | Snapshot : 810.2% / 40T / 2.4G | 20260505 07:31:34.531 | INFO | Finished read of next slice | 20260505 07:31:34.531 | INFO | Beginning read of next slice | 20260505 07:31:34.624 | INFO | Sending progress 0.616774 | 20260505 07:31:34.716 | INFO | Finished read of next slice | 20260505 07:31:34.721 | INFO | Final Performance Profiling Results for READ_PROFILES: (reported in milliseconds) | 20260505 07:31:34.721 | INFO | PerfReport: Gathered 4 samples. | 20260505 07:31:34.721 | INFO | PerfReport: % Compute, FullMean/OutlierMean FullDev/OutlierDev | 20260505 07:31:34.721 | INFO | PerfReport: Full Execution -- 1.27e+03 / 1.66e+03, 8.25e+02 / 6.76e+02 | 20260505 07:31:34.721 | INFO | PerfReport: 0.00%, TOTAL -- 3.55e-04 / 4.88e-04, 4.28e-04 / 6.91e-04 | 20260505 07:31:34.721 | INFO | PerfReport: 99.98%, READ_DATA -- 1.27e+03 / 1.66e+03, 8.25e+02 / 6.76e+02 | 20260505 07:31:34.721 | INFO | PerfReport: 0.02%, SEND_DATA -- 2.26e-01 / 2.31e-01, 1.25e-01 / 3.25e-02 | 20260505 07:31:35.624 | INFO | Sending progress 0.833447 | 20260505 07:31:36.625 | INFO | Sending progress 0.999990 | 20260505 07:31:36.732 | INFO | Closing BAM files | 20260505 07:31:36.732 | INFO | Writing PBI files | 20260505 07:31:37.732 | INFO | Corrected missing adapter (>35% per ZMW) in 4 ZMWs, 0.0511117% of 7826 total ZMWs with adapters | 20260505 07:31:37.732 | INFO | Corrected missed adapter (<=35% per ZMW) in 48 ZMWs, 0.61334% of 7826 total ZMWs with adapters | 20260505 07:31:37.732 | INFO | Corrected adapters in 52 ZMWs, 0.664452% of 7826 total ZMWs with adapters | 20260505 07:31:37.732 | INFO | Adapter Correction imputed 60 of 12024 total adapters (0.499002%) | 20260505 07:31:37.732 | INFO | Opening file "metadata/m84031_260504_231011_s1_basic_preview_4hr.sts.xml.tmp" | 20260505 07:31:37.793 | INFO | Renaming file "metadata/m84031_260504_231011_s1_basic_preview_4hr.sts.xml.tmp" -> "metadata/m84031_260504_231011_s1_basic_preview_4hr.sts.xml" | 20260505 07:31:37.804 | INFO | BAM files closed and PBIs written | 20260505 07:31:37.804 | INFO | Closing sts.h5 file | 20260505 07:31:37.806 | INFO | sts.h5 file closed and written | 20260505 07:31:37.806 | INFO | Finished ZMW processing 24576 | 20260505 07:31:37.806 | INFO | Finished | 20260505 07:31:37.806 | INFO | Final Performance Profiling Results for COMPUTE_PROFILES: (reported in milliseconds) | 20260505 07:31:37.806 | INFO | PerfReport: Gathered 6492 samples. | 20260505 07:31:37.806 | INFO | PerfReport: % Compute, FullMean/OutlierMean FullDev/OutlierDev | 20260505 07:31:37.806 | INFO | PerfReport: Full Execution -- 2.67e+01 / 3.63e+02, 7.71e+01 / 6.29e+01 | 20260505 07:31:37.806 | INFO | PerfReport: 36.73%, DATA_WAIT -- 9.81e+00 / 7.88e-01, 2.18e+00 / 1.06e+00 | 20260505 07:31:37.806 | INFO | PerfReport: 0.02%, DATA_MOVE -- 1.09e-01 / 2.93e-02, 4.59e-01 / 8.86e-03 | 20260505 07:31:37.806 | INFO | PerfReport: 0.00%, DATA_SEND -- 1.78e-02 / 2.06e-02, 4.84e-03 / 2.94e-03 | 20260505 07:31:37.806 | INFO | PerfReport: 7.26%, PARSE_BINARY -- 5.12e-01 / 5.26e-01, 1.68e+00 / 1.18e+00 | 20260505 07:31:37.806 | INFO | PerfReport: 3.54%, PROCESS_PACKETS -- 2.50e-01 / 3.08e-01, 1.39e+00 / 1.47e+00 | 20260505 07:31:37.806 | INFO | PerfReport: 5.29%, FIND_HQRF -- 3.73e-01 / 3.99e-01, 6.54e-01 / 4.66e-01 | 20260505 07:31:37.806 | INFO | PerfReport: 7.86%, FIND_INSERTS -- 5.55e-01 / 6.37e-01, 2.29e+00 / 2.26e+00 | 20260505 07:31:37.806 | INFO | PerfReport: 0.04%, PROD_STATS -- 2.78e-03 / 2.34e-03, 5.12e-02 / 2.44e-03 | 20260505 07:31:37.806 | INFO | PerfReport: 32.80%, FIND_SUBREAD -- 2.31e+00 / 2.48e+00, 4.79e+00 / 5.64e+00 | 20260505 07:31:37.806 | INFO | PerfReport: 5.33%, ZMW_STATS -- 3.76e-01 / 3.49e-01, 8.42e-01 / 5.56e-01 | 20260505 07:31:37.806 | INFO | PerfReport: 1.12%, FINALIZE -- 7.93e-02 / 1.21e-01, 9.37e-01 / 9.25e-01 | 20260505 07:31:37.806 | INFO | joining thread pool | 20260505 07:31:37.806 | INFO | joining loggingThread_ | 20260505 07:31:38.626 | INFO | joining done | 20260505 07:31:38.626 | INFO | ~ConvertBaz2BamDestroyed | 20260505 07:31:38.627 | INFO | Remap Stats: shiftedHqRegionStart = 15848 noStartOnLabelTransition = 0 noEndOnLabelTransition = 0 | 20260505 07:31:38.707 | INFO | Snapshot : 300.0% / 3T / 1.4G | 20260505 07:31:38.779 | INFO | Run Time : 10s 72ms | 20260505 07:31:38.779 | INFO | CPU Time : 1m 22s | 20260505 07:31:38.779 | INFO | Peak RSS : 3.060 GB | 20260505 07:31:38.779 | INFO | Exit code : 0