BQSR error
REQUIRED for all errors and issues:
a) GATK version used:
gatk/4.5.0.0
b) Exact command used:
I am running this shell script:
#! /usr/bin/env bash
# # lines starting with #$ is an instruction to the job scheduler
#$ -S /bin/bash # the shell language when run via the job scheduler [IMPORTANT]
#$ -cwd # job should run in the current working directory
#$ -j y # STDERR and STDOUT should be joined
#$ -R yes
#$ -l h_rt=80:00:00 # job requires up to 3 hours of runtime
#$ -r y # if job crashes, it should be restarted
module load CBI
module load gatk
input_bam="wgs_pre_edit/pre_edit_CKDN230037259-1A_HG57MDSX7-aligned_scratch_threaded_2_sorted_faster_dup_rg.bam"
ref="GRCh38_latest_genomic.fna"
output_bam="wgs_pre_edit/pre_edit_CKDN230037259-1A_HG57MDSX7-aligned_scratch_threaded_2_sorted_faster_dup_rg_bqsr_ncbi.bam"
known_var="GRCh38_latest_dbSNP_all.vcf"
gatk BaseRecalibrator \
-I "$input_bam" \
-R "$ref" \
--known-sites "$known_var" \
-O "$output_bam"
c) Entire program log:
This is the end of the program log:
16:36:46.188 INFO ProgressMeter - NC_000008.11:99187255 172.7 338951000 1962210.7
16:36:56.206 INFO ProgressMeter - NC_000008.11:100764277 172.9 339330000 1962507.8
16:37:06.218 INFO ProgressMeter - NC_000008.11:102278584 173.1 339712000 1962822.9
16:37:16.235 INFO ProgressMeter - NC_000008.11:103727498 173.2 340098000 1963159.4
16:37:26.241 INFO ProgressMeter - NC_000008.11:105344016 173.4 340475000 1963445.5
16:37:36.245 INFO ProgressMeter - NC_000008.11:107019845 173.6 340846000 1963696.9
16:37:46.245 INFO ProgressMeter - NC_000008.11:108662492 173.7 341219000 1963960.0
16:37:56.249 INFO ProgressMeter - NC_000008.11:110335323 173.9 341597000 1964250.6
16:38:06.250 INFO ProgressMeter - NC_000008.11:112084221 174.1 341967000 1964495.3
16:38:16.263 INFO ProgressMeter - NC_000008.11:113760150 174.2 342327000 1964679.9
16:38:26.288 INFO ProgressMeter - NC_000008.11:115403821 174.4 342713000 1965010.9
16:38:36.302 INFO ProgressMeter - NC_000008.11:117060763 174.6 343095000 1965320.5
16:38:44.921 INFO BaseRecalibrator - Shutting down engine
[May 7, 2024 at 4:39:05 PM PDT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 175.34 minutes.
Runtime.totalMemory()=5184159744
htsjdk.samtools.util.RuntimeIOException: Read error; BinaryCodec in readmode; file: /wynton/scratch/tanyasjain/wgs_pre_edit/pre_edit_CKDN230037259-1A_HG57MDSX7-aligned_scratch_threaded_2_sorted_faster_dup_rg.bam
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:423)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:394)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:282)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:882)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:856)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:850)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:818)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:591)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:570)
at org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.next(SAMRecordToReadIterator.java:27)
at org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.next(SAMRecordToReadIterator.java:13)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
at org.broadinstitute.hellbender.Main.main(Main.java:306)
Caused by: java.io.IOException: Communication error on send
at java.base/java.io.RandomAccessFile.readBytes(Native Method)
at java.base/java.io.RandomAccessFile.read(RandomAccessFile.java:405)
at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:85)
at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:582)
at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:571)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:536)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:479)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:469)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:207)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:342)
at java.base/java.io.DataInputStream.read(DataInputStream.java:151)
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:421)
... 27 more
-
Can you check if your input bam file is valid and not corrupt? You can use
gatk ValidateSamFile
for this purpose.
Regards.
-
[Mon May 13 13:04:56 PDT 2024] Executing as tanyajain@qb3-id286.wynton.ucsf.edu on Linux 4.18.0-513.24.1.el8_9.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.10+7-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.5.0.0
WARNING 2024-05-13 13:04:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
INFO 2024-05-13 13:05:33 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:00:36s. Time for last 10,000,000: 36s. Last read position: NC_000001.11:33,821,203
INFO 2024-05-13 13:06:09 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 36s. Last read position: NC_000001.11:66,488,788
INFO 2024-05-13 13:06:45 SamFileValidator Validated Read 30,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 35s. Last read position: NC_000001.11:101,838,604
INFO 2024-05-13 13:07:27 SamFileValidator Validated Read 40,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 42s. Last read position: NC_000001.11:143,233,049
INFO 2024-05-13 13:08:03 SamFileValidator Validated Read 50,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 36s. Last read position: NC_000001.11:174,111,759
INFO 2024-05-13 13:08:39 SamFileValidator Validated Read 60,000,000 records. Elapsed time: 00:03:43s. Time for last 10,000,000: 35s. Last read position: NC_000001.11:209,667,289
INFO 2024-05-13 13:09:15 SamFileValidator Validated Read 70,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 35s. Last read position: NC_000001.11:244,730,101
INFO 2024-05-13 13:09:53 SamFileValidator Validated Read 80,000,000 records. Elapsed time: 00:04:56s. Time for last 10,000,000: 38s. Last read position: NC_000002.12:30,386,018
INFO 2024-05-13 13:10:31 SamFileValidator Validated Read 90,000,000 records. Elapsed time: 00:05:34s. Time for last 10,000,000: 37s. Last read position: NC_000002.12:61,130,930
INFO 2024-05-13 13:11:07 SamFileValidator Validated Read 100,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 35s. Last read position: NC_000002.12:96,420,433
INFO 2024-05-13 13:11:44 SamFileValidator Validated Read 110,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 37s. Last read position: NC_000002.12:132,543,727
INFO 2024-05-13 13:12:19 SamFileValidator Validated Read 120,000,000 records. Elapsed time: 00:07:22s. Time for last 10,000,000: 35s. Last read position: NC_000002.12:168,288,973
INFO 2024-05-13 13:12:55 SamFileValidator Validated Read 130,000,000 records. Elapsed time: 00:07:58s. Time for last 10,000,000: 35s. Last read position: NC_000002.12:203,121,485
INFO 2024-05-13 13:13:29 SamFileValidator Validated Read 140,000,000 records. Elapsed time: 00:08:33s. Time for last 10,000,000: 34s. Last read position: NC_000002.12:238,293,608
INFO 2024-05-13 13:14:08 SamFileValidator Validated Read 150,000,000 records. Elapsed time: 00:09:11s. Time for last 10,000,000: 38s. Last read position: NC_000003.12:31,825,311
INFO 2024-05-13 13:14:43 SamFileValidator Validated Read 160,000,000 records. Elapsed time: 00:09:47s. Time for last 10,000,000: 35s. Last read position: NC_000003.12:65,285,115
INFO 2024-05-13 13:15:19 SamFileValidator Validated Read 170,000,000 records. Elapsed time: 00:10:22s. Time for last 10,000,000: 35s. Last read position: NC_000003.12:101,627,160
INFO 2024-05-13 13:15:53 SamFileValidator Validated Read 180,000,000 records. Elapsed time: 00:10:57s. Time for last 10,000,000: 34s. Last read position: NC_000003.12:136,424,160
INFO 2024-05-13 13:16:29 SamFileValidator Validated Read 190,000,000 records. Elapsed time: 00:11:32s. Time for last 10,000,000: 35s. Last read position: NC_000003.12:171,781,706
INFO 2024-05-13 13:17:07 SamFileValidator Validated Read 200,000,000 records. Elapsed time: 00:12:10s. Time for last 10,000,000: 37s. Last read position: NC_000004.12:7,663,131
INFO 2024-05-13 13:17:43 SamFileValidator Validated Read 210,000,000 records. Elapsed time: 00:12:46s. Time for last 10,000,000: 36s. Last read position: NC_000004.12:44,377,226
INFO 2024-05-13 13:18:20 SamFileValidator Validated Read 220,000,000 records. Elapsed time: 00:13:24s. Time for last 10,000,000: 37s. Last read position: NC_000004.12:73,171,074
INFO 2024-05-13 13:18:56 SamFileValidator Validated Read 230,000,000 records. Elapsed time: 00:13:59s. Time for last 10,000,000: 35s. Last read position: NC_000004.12:107,845,544
INFO 2024-05-13 13:19:33 SamFileValidator Validated Read 240,000,000 records. Elapsed time: 00:14:36s. Time for last 10,000,000: 36s. Last read position: NC_000004.12:143,514,853
INFO 2024-05-13 13:20:08 SamFileValidator Validated Read 250,000,000 records. Elapsed time: 00:15:12s. Time for last 10,000,000: 35s. Last read position: NC_000004.12:180,068,205
INFO 2024-05-13 13:20:49 SamFileValidator Validated Read 260,000,000 records. Elapsed time: 00:15:52s. Time for last 10,000,000: 40s. Last read position: NC_000005.10:25,911,372
INFO 2024-05-13 13:21:28 SamFileValidator Validated Read 270,000,000 records. Elapsed time: 00:16:31s. Time for last 10,000,000: 38s. Last read position: NC_000005.10:53,736,181
INFO 2024-05-13 13:22:03 SamFileValidator Validated Read 280,000,000 records. Elapsed time: 00:17:07s. Time for last 10,000,000: 35s. Last read position: NC_000005.10:89,647,335
INFO 2024-05-13 13:22:39 SamFileValidator Validated Read 290,000,000 records. Elapsed time: 00:17:42s. Time for last 10,000,000: 35s. Last read position: NC_000005.10:125,277,653
INFO 2024-05-13 13:23:15 SamFileValidator Validated Read 300,000,000 records. Elapsed time: 00:18:19s. Time for last 10,000,000: 36s. Last read position: NC_000005.10:159,465,979
INFO 2024-05-13 13:23:54 SamFileValidator Validated Read 310,000,000 records. Elapsed time: 00:18:58s. Time for last 10,000,000: 39s. Last read position: NC_000006.12:12,856,521
INFO 2024-05-13 13:24:31 SamFileValidator Validated Read 320,000,000 records. Elapsed time: 00:19:35s. Time for last 10,000,000: 36s. Last read position: NC_000006.12:50,646,654
INFO 2024-05-13 13:25:07 SamFileValidator Validated Read 330,000,000 records. Elapsed time: 00:20:10s. Time for last 10,000,000: 35s. Last read position: NC_000006.12:86,675,491
INFO 2024-05-13 13:25:46 SamFileValidator Validated Read 340,000,000 records. Elapsed time: 00:20:49s. Time for last 10,000,000: 38s. Last read position: NC_000006.12:121,606,374
INFO 2024-05-13 13:26:22 SamFileValidator Validated Read 350,000,000 records. Elapsed time: 00:21:26s. Time for last 10,000,000: 36s. Last read position: NC_000006.12:156,939,091
INFO 2024-05-13 13:27:01 SamFileValidator Validated Read 360,000,000 records. Elapsed time: 00:22:04s. Time for last 10,000,000: 38s. Last read position: NC_000007.14:21,324,941
INFO 2024-05-13 13:27:37 SamFileValidator Validated Read 370,000,000 records. Elapsed time: 00:22:40s. Time for last 10,000,000: 35s. Last read position: NC_000007.14:55,777,532
INFO 2024-05-13 13:28:11 SamFileValidator Validated Read 380,000,000 records. Elapsed time: 00:23:15s. Time for last 10,000,000: 34s. Last read position: NC_000007.14:90,019,589
INFO 2024-05-13 13:28:47 SamFileValidator Validated Read 390,000,000 records. Elapsed time: 00:23:51s. Time for last 10,000,000: 35s. Last read position: NC_000007.14:124,409,036
INFO 2024-05-13 13:29:28 SamFileValidator Validated Read 400,000,000 records. Elapsed time: 00:24:31s. Time for last 10,000,000: 40s. Last read position: NC_000008.11:577,875
INFO 2024-05-13 13:30:03 SamFileValidator Validated Read 410,000,000 records. Elapsed time: 00:25:06s. Time for last 10,000,000: 34s. Last read position: NC_000008.11:40,934,573
INFO 2024-05-13 13:30:37 SamFileValidator Validated Read 420,000,000 records. Elapsed time: 00:25:41s. Time for last 10,000,000: 34s. Last read position: NC_000008.11:75,246,444
INFO 2024-05-13 13:31:12 SamFileValidator Validated Read 430,000,000 records. Elapsed time: 00:26:15s. Time for last 10,000,000: 34s. Last read position: NC_000008.11:109,883,471
INFO 2024-05-13 13:31:49 SamFileValidator Validated Read 440,000,000 records. Elapsed time: 00:26:53s. Time for last 10,000,000: 37s. Last read position: NC_000009.12:1,418,442
INFO 2024-05-13 13:32:25 SamFileValidator Validated Read 450,000,000 records. Elapsed time: 00:27:28s. Time for last 10,000,000: 35s. Last read position: NC_000009.12:36,553,084
INFO 2024-05-13 13:33:00 SamFileValidator Validated Read 460,000,000 records. Elapsed time: 00:28:04s. Time for last 10,000,000: 35s. Last read position: NC_000009.12:87,422,703
INFO 2024-05-13 13:33:39 SamFileValidator Validated Read 470,000,000 records. Elapsed time: 00:28:43s. Time for last 10,000,000: 39s. Last read position: NC_000009.12:122,065,832
INFO 2024-05-13 13:34:21 SamFileValidator Validated Read 480,000,000 records. Elapsed time: 00:29:24s. Time for last 10,000,000: 41s. Last read position: NC_000010.11:16,790,442
INFO 2024-05-13 13:34:58 SamFileValidator Validated Read 490,000,000 records. Elapsed time: 00:30:01s. Time for last 10,000,000: 36s. Last read position: NC_000010.11:46,682,967
INFO 2024-05-13 13:35:33 SamFileValidator Validated Read 500,000,000 records. Elapsed time: 00:30:36s. Time for last 10,000,000: 35s. Last read position: NC_000010.11:81,869,417
INFO 2024-05-13 13:36:08 SamFileValidator Validated Read 510,000,000 records. Elapsed time: 00:31:11s. Time for last 10,000,000: 34s. Last read position: NC_000010.11:116,003,587
INFO 2024-05-13 13:36:47 SamFileValidator Validated Read 520,000,000 records. Elapsed time: 00:31:51s. Time for last 10,000,000: 39s. Last read position: NC_000011.10:17,231,034
INFO 2024-05-13 13:37:24 SamFileValidator Validated Read 530,000,000 records. Elapsed time: 00:32:27s. Time for last 10,000,000: 36s. Last read position: NC_000011.10:53,336,500
INFO 2024-05-13 13:38:00 SamFileValidator Validated Read 540,000,000 records. Elapsed time: 00:33:03s. Time for last 10,000,000: 36s. Last read position: NC_000011.10:87,210,723
INFO 2024-05-13 13:38:36 SamFileValidator Validated Read 550,000,000 records. Elapsed time: 00:33:39s. Time for last 10,000,000: 36s. Last read position: NC_000011.10:122,591,297
INFO 2024-05-13 13:39:17 SamFileValidator Validated Read 560,000,000 records. Elapsed time: 00:34:20s. Time for last 10,000,000: 40s. Last read position: NC_000012.12:22,770,027
INFO 2024-05-13 13:39:54 SamFileValidator Validated Read 570,000,000 records. Elapsed time: 00:34:58s. Time for last 10,000,000: 37s. Last read position: NC_000012.12:56,640,348
INFO 2024-05-13 13:40:34 SamFileValidator Validated Read 580,000,000 records. Elapsed time: 00:35:37s. Time for last 10,000,000: 39s. Last read position: NC_000012.12:92,152,211
INFO 2024-05-13 13:41:15 SamFileValidator Validated Read 590,000,000 records. Elapsed time: 00:36:19s. Time for last 10,000,000: 41s. Last read position: NC_000012.12:125,360,392
INFO 2024-05-13 13:41:55 SamFileValidator Validated Read 600,000,000 records. Elapsed time: 00:36:58s. Time for last 10,000,000: 39s. Last read position: NC_000013.11:43,293,524
INFO 2024-05-13 13:42:35 SamFileValidator Validated Read 610,000,000 records. Elapsed time: 00:37:39s. Time for last 10,000,000: 40s. Last read position: NC_000013.11:79,587,464
INFO 2024-05-13 13:43:21 SamFileValidator Validated Read 620,000,000 records. Elapsed time: 00:38:24s. Time for last 10,000,000: 45s. Last read position: NC_000014.9:18,351,481
INFO 2024-05-13 13:44:00 SamFileValidator Validated Read 630,000,000 records. Elapsed time: 00:39:04s. Time for last 10,000,000: 39s. Last read position: NC_000014.9:53,203,628
INFO 2024-05-13 13:44:38 SamFileValidator Validated Read 640,000,000 records. Elapsed time: 00:39:42s. Time for last 10,000,000: 38s. Last read position: NC_000014.9:87,198,510
INFO 2024-05-13 13:45:26 SamFileValidator Validated Read 650,000,000 records. Elapsed time: 00:40:30s. Time for last 10,000,000: 47s. Last read position: NC_000015.10:35,828,816
INFO 2024-05-13 13:46:04 SamFileValidator Validated Read 660,000,000 records. Elapsed time: 00:41:07s. Time for last 10,000,000: 37s. Last read position: NC_000015.10:69,177,868
INFO 2024-05-13 13:46:49 SamFileValidator Validated Read 670,000,000 records. Elapsed time: 00:41:52s. Time for last 10,000,000: 44s. Last read position: NC_000016.10:1,720,520
INFO 2024-05-13 13:47:27 SamFileValidator Validated Read 680,000,000 records. Elapsed time: 00:42:30s. Time for last 10,000,000: 38s. Last read position: NC_000016.10:36,472,789
INFO 2024-05-13 13:48:05 SamFileValidator Validated Read 690,000,000 records. Elapsed time: 00:43:08s. Time for last 10,000,000: 38s. Last read position: NC_000016.10:74,006,011
INFO 2024-05-13 13:48:46 SamFileValidator Validated Read 700,000,000 records. Elapsed time: 00:43:50s. Time for last 10,000,000: 41s. Last read position: NC_000017.11:16,933,057
INFO 2024-05-13 13:49:28 SamFileValidator Validated Read 710,000,000 records. Elapsed time: 00:44:31s. Time for last 10,000,000: 41s. Last read position: NC_000017.11:51,205,185
INFO 2024-05-13 13:50:09 SamFileValidator Validated Read 720,000,000 records. Elapsed time: 00:45:12s. Time for last 10,000,000: 40s. Last read position: NT_187384.1:24,629
INFO 2024-05-13 13:50:50 SamFileValidator Validated Read 730,000,000 records. Elapsed time: 00:45:54s. Time for last 10,000,000: 41s. Last read position: NC_000018.10:32,341,635
INFO 2024-05-13 13:51:29 SamFileValidator Validated Read 740,000,000 records. Elapsed time: 00:46:33s. Time for last 10,000,000: 39s. Last read position: NC_000018.10:68,731,356
INFO 2024-05-13 13:52:17 SamFileValidator Validated Read 750,000,000 records. Elapsed time: 00:47:21s. Time for last 10,000,000: 47s. Last read position: NC_000019.10:22,100,074
INFO 2024-05-13 13:52:57 SamFileValidator Validated Read 760,000,000 records. Elapsed time: 00:48:00s. Time for last 10,000,000: 39s. Last read position: NC_000019.10:52,927,239
INFO 2024-05-13 13:53:42 SamFileValidator Validated Read 770,000,000 records. Elapsed time: 00:48:46s. Time for last 10,000,000: 45s. Last read position: NC_000020.11:27,933,349
INFO 2024-05-13 13:54:21 SamFileValidator Validated Read 780,000,000 records. Elapsed time: 00:49:24s. Time for last 10,000,000: 38s. Last read position: NC_000020.11:58,008,386
INFO 2024-05-13 13:55:03 SamFileValidator Validated Read 790,000,000 records. Elapsed time: 00:50:06s. Time for last 10,000,000: 42s. Last read position: NC_000021.9:30,657,466
INFO 2024-05-13 13:55:43 SamFileValidator Validated Read 800,000,000 records. Elapsed time: 00:50:47s. Time for last 10,000,000: 40s. Last read position: NC_000022.11:29,006,632
INFO 2024-05-13 13:56:26 SamFileValidator Validated Read 810,000,000 records. Elapsed time: 00:51:29s. Time for last 10,000,000: 42s. Last read position: NC_000023.11:14,486,563
INFO 2024-05-13 13:57:02 SamFileValidator Validated Read 820,000,000 records. Elapsed time: 00:52:05s. Time for last 10,000,000: 36s. Last read position: NC_000023.11:83,247,053
INFO 2024-05-13 13:57:39 SamFileValidator Validated Read 830,000,000 records. Elapsed time: 00:52:43s. Time for last 10,000,000: 37s. Last read position: NC_000023.11:152,632,073
INFO 2024-05-13 13:58:27 SamFileValidator Validated Read 840,000,000 records. Elapsed time: 00:53:30s. Time for last 10,000,000: 47s. Last read position: NT_187425.1:108,771
INFO 2024-05-13 13:59:19 SamFileValidator Validated Read 850,000,000 records. Elapsed time: 00:54:22s. Time for last 10,000,000: 52s. Last read position: NW_025791781.1:37,649
INFO 2024-05-13 14:00:03 SamFileValidator Validated Read 860,000,000 records. Elapsed time: 00:55:07s. Time for last 10,000,000: 44s. Last read position: NW_025791818.1:496,821
INFO 2024-05-13 14:00:50 SamFileValidator Validated Read 870,000,000 records. Elapsed time: 00:55:53s. Time for last 10,000,000: 46s. Last read position: NT_167248.2:1,892,457
No errors found
[Mon May 13 14:24:14 PDT 2024] picard.sam.ValidateSamFile done. Elapsed time: 79.30 minutes.
Runtime.totalMemory()=2583691264
Tool returned:
0
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Im running the recalibration script again, and seemed to be getting further along (not crashing at NC_000008.11:117060763), though still curious what the issue could've been
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It is good to hear that bam file is intact and your analysis is going on. It could be a disconnection or IO error somewhere within your compute environment that could cause read issues.
Regards.
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