| 20260506 12:41:33.151 | INFO | Snapshot : (Legend) % CPU / Threads / ResMem GiB | 20260506 12:41:33.151 | INFO | Snapshot : 0.0% / 3T / 0.0G | 20260506 12:41:33.151 | 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_260506_033729_s1/metadata/m84031_260506_033729_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_260506_033729_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=3aff3ffb-84a8-4d3d-9934-39ea4705feda --silent --whitelistZmwId=0 --samplePercent=100 --zmwBatchMB=250 --zmwHeaderBatchMB=10 --maxOutputQueueMB=5000 --log-level=INFO --log-file=/data/icc/m84031_260506_033729_s1/metadata/m84031_260506_033729_s1_basic_preview_4hr.baz2bam.log /data/nrta/0/m84031_260506_033729_s1/pb_internal/baz/m84031_260506_033729_s1_basic_preview.baz | 20260506 12:41:33.152 | INFO | Start | 20260506 12:41:33.152 | 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_260506_033729_s1/metadata/m84031_260506_033729_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_260506_033729_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=3aff3ffb-84a8-4d3d-9934-39ea4705feda --silent --whitelistZmwId=0 --samplePercent=100 --zmwBatchMB=250 --zmwHeaderBatchMB=10 --maxOutputQueueMB=5000 --log-level=INFO --log-file=/data/icc/m84031_260506_033729_s1/metadata/m84031_260506_033729_s1_basic_preview_4hr.baz2bam.log /data/nrta/0/m84031_260506_033729_s1/pb_internal/baz/m84031_260506_033729_s1_basic_preview.baz | 20260506 12:41:33.152 | INFO | commit hash: 2dc54f5a66f39b94662202d5514157d553e25f7d | 20260506 12:41:33.152 | INFO | commit date: 2026-01-13 11:49:20 +0100 | 20260506 12:41:33.152 | INFO | Version: release/kestrel-13.5_2dc54f5a66f39b94662202d5514157d553e25f7d | 20260506 12:41:33.152 | INFO | Roughly processing the first 2147483647 ZMWs, up to a slice boundary... | 20260506 12:41:33.464 | INFO | Parsing "/data/icc/m84031_260506_033729_s1/metadata/m84031_260506_033729_s1_basic_preview_4hr.metadata.xml" | 20260506 12:41:33.466 | 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}} | 20260506 12:41:33.930 | INFO | 24 adapter callers have been configured with the standard method | 20260506 12:41:33.931 | INFO | Created BAM Header comment:{ "collection_metadata_xml" : "", "dataset_uuid" : "bb760677-ba7e-44bd-8c36-f064bb17bd60", "external_resources" : [ { "file_name" : "../metadata/m84031_260506_033729_s1_basic_preview_4hr.sts.xml", "meta_type" : "PacBio.SubreadFile.ChipStatsFile" } ], "name" : "baz2bam_ccs_sideband", "subreadset_name" : "Acq14-Cell5", "version" : "1.2", "zmws" : 24576 } | 20260506 12:41:33.931 | INFO | bam file: - | 20260506 12:41:33.931 | INFO | bamThreads = 8 | 20260506 12:41:33.931 | INFO | Writing streaming BAM file to stdout | 20260506 12:41:33.943 | INFO | ZOFFSET_CART_HMM configured | 20260506 12:41:33.943 | INFO | Creating sts.h5 file "pb_internal/m84031_260506_033729_s1_basic_preview_4hr.sts.h5" with parameters numHoles:24576 numAnalogs:4 numFilters:1 | 20260506 12:41:33.946 | INFO | Starting Baz2bam. MovieName: /data/nrta/0/m84031_260506_033729_s1/pb_internal/baz/m84031_260506_033729_s1_basic_preview.baz, BaseCallerVersion: 5.0.0, BazWriterVersion: 0.0.0, BazVersion: 2.6.2, OutputPrefix: "m84031_260506_033729_s1_basic_preview_4hr", ProdFileLayout: Kestrel, Baz2bamVersion: release/kestrel-13.5_2dc54f5a66f39b94662202d5514157d553e25f7d | 20260506 12:41:33.946 | INFO | Spawn 24 workers | 20260506 12:41:34.189 | INFO | Beginning read of next slice | 20260506 12:41:34.189 | INFO | OOM score went from -1 to 1268 | 20260506 12:41:35.189 | INFO | OOM score went from 1268 to 1270 | 20260506 12:41:35.453 | INFO | Finished read of next slice | 20260506 12:41:35.453 | WARN | Anomalous profiling event (reported in ms): | 20260506 12:41:35.453 | WARN | READ_PROFILES measured slower than specified threshold of 3.40282e+38 standard deviations | 20260506 12:41:35.453 | WARN | IDs: Historic mean +- stdev, [ Current Measurements ] | 20260506 12:41:35.453 | WARN | ---------------------------------------------------------- | 20260506 12:41:35.453 | WARN | Full: 0.00e+00 +- 0.00e+00, [ 1.26e+03 ] | 20260506 12:41:35.453 | WARN | TOTAL: 1.22e-03 +- 0.00e+00, [ 1.22e-03 ] | 20260506 12:41:35.453 | WARN | READ_DATA: 1.26e+03 +- 0.00e+00, [ 1.26e+03 ] | 20260506 12:41:35.453 | WARN | SEND_DATA: 2.20e-01 +- 0.00e+00, [ 2.20e-01 ] | 20260506 12:41:35.453 | INFO | Beginning read of next slice | 20260506 12:41:36.189 | INFO | OOM score went from 1270 to 1271 | 20260506 12:41:36.189 | INFO | Sending progress 0.097655 | 20260506 12:41:37.190 | INFO | Sending progress 0.250242 | 20260506 12:41:37.998 | INFO | Finished read of next slice | 20260506 12:41:37.999 | WARN | Anomalous profiling event (reported in ms): | 20260506 12:41:37.999 | WARN | READ_PROFILES measured slower than specified threshold of 3.40282e+38 standard deviations | 20260506 12:41:37.999 | WARN | IDs: Historic mean +- stdev, [ Current Measurements ] | 20260506 12:41:37.999 | WARN | ---------------------------------------------------------- | 20260506 12:41:37.999 | WARN | Full: 1.26e+03 +- 0.00e+00, [ 2.55e+03 ] | 20260506 12:41:37.999 | WARN | TOTAL: 1.34e-03 +- 1.73e-04, [ 1.46e-03 ] | 20260506 12:41:37.999 | WARN | READ_DATA: 1.90e+03 +- 9.06e+02, [ 2.54e+03 ] | 20260506 12:41:37.999 | WARN | SEND_DATA: 2.47e-01 +- 3.93e-02, [ 2.75e-01 ] | 20260506 12:41:37.999 | INFO | Beginning read of next slice | 20260506 12:41:38.151 | INFO | Snapshot : 612.2% / 40T / 2.2G | 20260506 12:41:38.192 | INFO | Sending progress 0.334388 | 20260506 12:41:39.195 | INFO | Sending progress 0.554112 | 20260506 12:41:39.868 | INFO | Finished read of next slice | 20260506 12:41:39.872 | INFO | Final Performance Profiling Results for READ_PROFILES: (reported in milliseconds) | 20260506 12:41:39.872 | INFO | PerfReport: Gathered 3 samples. | 20260506 12:41:39.872 | INFO | PerfReport: % Compute, FullMean/OutlierMean FullDev/OutlierDev | 20260506 12:41:39.872 | INFO | PerfReport: Full Execution -- 1.89e+03 / 1.90e+03, 6.41e+02 / 9.06e+02 | 20260506 12:41:39.872 | INFO | PerfReport: 0.00%, TOTAL -- 1.02e-03 / 1.34e-03, 5.77e-04 / 1.73e-04 | 20260506 12:41:39.872 | INFO | PerfReport: 99.98%, READ_DATA -- 1.89e+03 / 1.90e+03, 6.41e+02 / 9.06e+02 | 20260506 12:41:39.872 | INFO | PerfReport: 0.02%, SEND_DATA -- 3.38e-01 / 2.47e-01, 1.59e-01 / 3.93e-02 | 20260506 12:41:40.199 | INFO | Sending progress 0.737582 | 20260506 12:41:41.208 | INFO | Sending progress 0.932852 | 20260506 12:41:41.888 | INFO | Closing BAM files | 20260506 12:41:41.888 | INFO | Writing PBI files | 20260506 12:41:42.212 | INFO | Sending progress 0.999990 | 20260506 12:41:42.889 | INFO | Corrected missing adapter (>35% per ZMW) in 15 ZMWs, 0.216076% of 6942 total ZMWs with adapters | 20260506 12:41:42.889 | INFO | Corrected missed adapter (<=35% per ZMW) in 43 ZMWs, 0.619418% of 6942 total ZMWs with adapters | 20260506 12:41:42.889 | INFO | Corrected adapters in 58 ZMWs, 0.835494% of 6942 total ZMWs with adapters | 20260506 12:41:42.889 | INFO | Adapter Correction imputed 80 of 10738 total adapters (0.745018%) | 20260506 12:41:42.889 | INFO | Opening file "metadata/m84031_260506_033729_s1_basic_preview_4hr.sts.xml.tmp" | 20260506 12:41:42.938 | INFO | Renaming file "metadata/m84031_260506_033729_s1_basic_preview_4hr.sts.xml.tmp" -> "metadata/m84031_260506_033729_s1_basic_preview_4hr.sts.xml" | 20260506 12:41:42.949 | INFO | BAM files closed and PBIs written | 20260506 12:41:42.949 | INFO | Closing sts.h5 file | 20260506 12:41:42.952 | INFO | sts.h5 file closed and written | 20260506 12:41:42.952 | INFO | Finished ZMW processing 24576 | 20260506 12:41:42.952 | INFO | Finished | 20260506 12:41:42.952 | INFO | Final Performance Profiling Results for COMPUTE_PROFILES: (reported in milliseconds) | 20260506 12:41:42.952 | INFO | PerfReport: Gathered 7018 samples. | 20260506 12:41:42.952 | INFO | PerfReport: % Compute, FullMean/OutlierMean FullDev/OutlierDev | 20260506 12:41:42.952 | INFO | PerfReport: Full Execution -- 2.67e+01 / 3.55e+02, 7.95e+01 / 2.78e+01 | 20260506 12:41:42.952 | INFO | PerfReport: 37.06%, DATA_WAIT -- 9.89e+00 / 3.05e-02, 2.19e+00 / 1.57e-03 | 20260506 12:41:42.952 | INFO | PerfReport: 0.08%, DATA_MOVE -- 4.43e-01 / 2.20e-02, 1.93e+00 / 1.56e-03 | 20260506 12:41:42.952 | INFO | PerfReport: 0.01%, DATA_SEND -- 3.35e-02 / 1.81e-02, 1.80e-01 / 5.93e-04 | 20260506 12:41:42.952 | INFO | PerfReport: 9.85%, PARSE_BINARY -- 7.51e-01 / 3.61e-01, 2.38e+00 / 4.35e-01 | 20260506 12:41:42.952 | INFO | PerfReport: 3.46%, PROCESS_PACKETS -- 2.64e-01 / 2.80e-01, 1.43e+00 / 1.26e+00 | 20260506 12:41:42.952 | INFO | PerfReport: 4.85%, FIND_HQRF -- 3.70e-01 / 3.91e-01, 6.09e-01 / 6.21e-01 | 20260506 12:41:42.952 | INFO | PerfReport: 7.29%, FIND_INSERTS -- 5.56e-01 / 5.63e-01, 2.58e+00 / 1.69e+00 | 20260506 12:41:42.952 | INFO | PerfReport: 0.04%, PROD_STATS -- 2.72e-03 / 2.22e-03, 6.90e-02 / 3.55e-03 | 20260506 12:41:42.952 | INFO | PerfReport: 31.08%, FIND_SUBREAD -- 2.37e+00 / 2.55e+00, 5.70e+00 / 6.83e+00 | 20260506 12:41:42.952 | INFO | PerfReport: 5.05%, ZMW_STATS -- 3.85e-01 / 3.89e-01, 8.64e-01 / 8.04e-01 | 20260506 12:41:42.952 | INFO | PerfReport: 1.24%, FINALIZE -- 9.46e-02 / 2.00e-01, 1.19e+00 / 1.60e+00 | 20260506 12:41:42.952 | INFO | joining thread pool | 20260506 12:41:42.952 | INFO | joining loggingThread_ | 20260506 12:41:43.151 | INFO | Snapshot : 400.0% / 4T / 2.0G | 20260506 12:41:43.213 | INFO | joining done | 20260506 12:41:43.213 | INFO | ~ConvertBaz2BamDestroyed | 20260506 12:41:43.213 | INFO | Remap Stats: shiftedHqRegionStart = 13673 noStartOnLabelTransition = 0 noEndOnLabelTransition = 0 | 20260506 12:41:43.411 | INFO | Run Time : 10s 260ms | 20260506 12:41:43.411 | INFO | CPU Time : 1m 21s | 20260506 12:41:43.411 | INFO | Peak RSS : 2.889 GB | 20260506 12:41:43.411 | INFO | Exit code : 0