Hi,

I'm Yuan. I had a problem when I was using the Mutect2, GATK/4.1.0.0-Java-1.8.0_144 to identify tumor somatic mutations in canine.

The running of the program always stop at 'chr6'. And I checked all my inputs, nothing seems wrong to me. So I wonder does anyone had the same problem? Here are my codes and error messages. I really appreciate your help!!

gatk --java-options "-Xmx72G" Mutect2 \
-R $reference/canFam3.fa \
-I ${Mutect2_Test}/SRR7780923_rg_added_sorted_dedupped_removed.realigned.bam \
-I ${Mutect2_Test}/SRR7780922_rg_added_sorted_dedupped_removed.realigned.bam \
-normal $Normal_sample \
--panel-of-normals $MuTect2_source/pon.vcf.gz \
--initial-tumor-lod 2.0 --normal-lod 2.2 --tumor-lod-to-emit 3.0 --pcr-indel-model CONSERVATIVE \
-L $reference/Canis_familiaris.CanFam3.1.99.gtf-chr1-38X-CDS-forDepthOfCoverage.interval_list \
-O $mutect2_result/New-realigned-CMT-2_MuTect2_GATK4.vcf

Using GATK jar /usr/local/apps/eb/GATK/4.1.0.0-Java-1.8.0_144/gatk-package-4.1.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx72G -jar /usr/local/apps/eb/GATK/4.1.0.0-Java-1.8.0_144/gatk-package-4.1.0.0-local.jar Mutect2 -R /work/szlab/Lab_shared_PanCancer/source/canFam3.fa -I /scratch/kh31516/MuTect2/Test/SRR7780923_rg_added_sorted_dedupped_removed.realigned.bam -I /scratch/kh31516/MuTect2/Test/SRR7780922_rg_added_sorted_dedupped_removed.realigned.bam -normal SRR7780922_normal --panel-of-normals /scratch/kh31516/MuTect2/source/pon.vcf.gz --initial-tumor-lod 2.0 --normal-lod 2.2 --tumor-lod-to-emit 3.0 --pcr-indel-model CONSERVATIVE -L /work/szlab/Lab_shared_PanCancer/source/Canis_familiaris.CanFam3.1.99.gtf-chr1-38X-CDS-forDepthOfCoverage.interval_list -O /scratch/yf94402/Pan_cancer/script/Mutect2/New-realigned-CMT-2_MuTect2_GATK4.vcf
12:44:36.014 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/apps/eb/GATK/4.1.0.0-Java-1.8.0_144/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:44:37.839 INFO Mutect2 - ------------------------------------------------------------
12:44:37.840 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.0.0
12:44:37.840 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
12:44:37.841 INFO Mutect2 - Executing as yf94402@sapelo2-sub5.ecompute on Linux v3.10.0-862.14.4.el7.x86_64 amd64
12:44:37.841 INFO Mutect2 - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_144-b01
12:44:37.841 INFO Mutect2 - Start Date/Time: April 27, 2020 12:44:35 PM EDT
12:44:37.841 INFO Mutect2 - ------------------------------------------------------------
12:44:37.841 INFO Mutect2 - ------------------------------------------------------------
12:44:37.842 INFO Mutect2 - HTSJDK Version: 2.18.2
12:44:37.842 INFO Mutect2 - Picard Version: 2.18.25
12:44:37.842 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:44:37.842 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:44:37.842 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:44:37.842 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:44:37.842 INFO Mutect2 - Deflater: IntelDeflater
12:44:37.842 INFO Mutect2 - Inflater: IntelInflater
12:44:37.842 INFO Mutect2 - GCS max retries/reopens: 20
12:44:37.842 INFO Mutect2 - Requester pays: disabled
12:44:37.842 INFO Mutect2 - Initializing engine
WARNING: BAM index file /scratch/kh31516/MuTect2/Test/SRR7780923_rg_added_sorted_dedupped_removed.realigned.bai is older than BAM /scratch/kh31516/MuTect2/Test/SRR7780923_rg_added_sorted_dedupped_removed.realigned.bam
12:44:38.223 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/kh31516/MuTect2/source/pon.vcf.gz
12:44:39.145 INFO IntervalArgumentCollection - Processing 35407612 bp from intervals
12:44:39.279 INFO Mutect2 - Done initializing engine
12:44:39.305 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/apps/eb/GATK/4.1.0.0-Java-1.8.0_144/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
12:44:39.307 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/local/apps/eb/GATK/4.1.0.0-Java-1.8.0_144/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
12:44:39.348 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
12:44:39.349 INFO IntelPairHmm - Available threads: 16
12:44:39.349 INFO IntelPairHmm - Requested threads: 4
12:44:39.349 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
12:44:39.377 INFO ProgressMeter - Starting traversal
12:44:39.377 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
12:44:49.433 INFO ProgressMeter - chr1:16818634 0.2 830 4952.8
12:44:59.462 INFO ProgressMeter - chr1:31149748 0.3 1840 5496.6
12:45:09.494 INFO ProgressMeter - chr1:42603918 0.5 2700 5379.2
12:45:19.567 INFO ProgressMeter - chr1:56814501 0.7 3800 5673.1
12:45:29.595 INFO ProgressMeter - chr1:70512666 0.8 4760 5687.2
12:45:39.611 INFO ProgressMeter - chr1:87194952 1.0 5800 5777.9
12:45:49.650 INFO ProgressMeter - chr1:98904376 1.2 6860 5857.2
12:45:59.667 INFO ProgressMeter - chr1:102339880 1.3 7840 5858.8
12:46:09.709 INFO ProgressMeter - chr1:106706609 1.5 9320 6190.5
12:46:19.767 INFO ProgressMeter - chr1:109761765 1.7 10680 6383.1
12:46:29.802 INFO ProgressMeter - chr1:112636634 1.8 11820 6422.5
12:46:39.847 INFO ProgressMeter - chr1:115997983 2.0 13170 6559.3
12:46:49.967 INFO ProgressMeter - chr1:121537346 2.2 14290 6565.6
12:47:00.030 INFO ProgressMeter - chr2:18084088 2.3 15380 6560.8
12:47:10.087 INFO ProgressMeter - chr2:30531129 2.5 16390 6525.1
12:47:20.110 INFO ProgressMeter - chr2:42328743 2.7 17730 6618.4
12:47:30.183 INFO ProgressMeter - chr2:54700775 2.8 18690 6565.3
12:47:40.304 INFO ProgressMeter - chr2:64256631 3.0 19910 6602.7
12:47:50.316 INFO ProgressMeter - chr2:72582456 3.2 21120 6636.7
12:48:00.342 INFO ProgressMeter - chr2:77528881 3.3 22320 6663.9
12:48:10.668 INFO ProgressMeter - chr2:84104353 3.5 23480 6667.6
12:48:20.788 INFO ProgressMeter - chr3:13949148 3.7 24510 6641.9
12:48:30.843 INFO ProgressMeter - chr3:27739121 3.9 25310 6560.8
12:48:41.264 INFO ProgressMeter - chr3:40508384 4.0 26370 6541.1
12:48:51.280 INFO ProgressMeter - chr3:54597089 4.2 27590 6571.6
12:49:01.317 INFO ProgressMeter - chr3:62818876 4.4 28890 6617.5
12:49:11.358 INFO ProgressMeter - chr3:75594733 4.5 29860 6587.2
12:49:21.437 INFO ProgressMeter - chr4:3524920 4.7 30870 6566.7
12:49:31.476 INFO ProgressMeter - chr4:14100847 4.9 31870 6546.4
12:49:41.567 INFO ProgressMeter - chr4:23779314 5.0 32810 6514.4
12:49:51.585 INFO ProgressMeter - chr4:35904065 5.2 33970 6528.3
12:50:01.689 INFO ProgressMeter - chr4:52657362 5.4 35140 6541.5
12:50:11.701 INFO ProgressMeter - chr4:62208914 5.5 36240 6543.0
12:50:21.748 INFO ProgressMeter - chr4:72846025 5.7 37190 6517.5
12:50:31.755 INFO ProgressMeter - chr5:5896880 5.9 38170 6499.3
12:50:41.760 INFO ProgressMeter - chr5:14277915 6.0 39120 6477.1
12:50:51.802 INFO ProgressMeter - chr5:21205552 6.2 40270 6487.7
12:51:01.826 INFO ProgressMeter - chr5:30542326 6.4 41270 6474.6
12:51:11.841 INFO ProgressMeter - chr5:32959573 6.5 42660 6521.9
12:51:21.913 INFO ProgressMeter - chr5:40830677 6.7 43930 6548.0
12:51:31.952 INFO ProgressMeter - chr5:48858646 6.9 45020 6547.2
12:51:41.986 INFO ProgressMeter - chr5:58164780 7.0 46390 6586.2
12:51:52.119 INFO ProgressMeter - chr5:65498142 7.2 47810 6628.9
12:52:02.173 INFO ProgressMeter - chr5:77339256 7.4 49060 6647.8
12:52:12.179 INFO ProgressMeter - chr5:82338487 7.5 50200 6651.9
12:52:22.493 INFO ProgressMeter - chr6:8583316 7.7 51360 6654.1
12:52:32.657 INFO ProgressMeter - chr6:12008602 7.9 52580 6665.8
12:52:42.729 INFO ProgressMeter - chr6:17512441 8.1 53820 6680.8
12:52:52.858 INFO ProgressMeter - chr6:23125927 8.2 54970 6683.5
12:53:02.907 INFO ProgressMeter - chr6:30069578 8.4 56100 6684.8
12:53:12.957 INFO ProgressMeter - chr6:38432205 8.6 57360 6701.2
12:53:23.007 INFO ProgressMeter - chr6:41947219 8.7 58870 6745.6
12:53:33.076 INFO ProgressMeter - chr6:55155875 8.9 59910 6735.3
12:53:43.091 INFO ProgressMeter - chr6:63510811 9.1 60790 6708.3
12:53:49.628 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.130989607
12:53:49.628 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 19.088335496000003
12:53:49.628 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 25.67 sec
12:53:49.628 INFO Mutect2 - Shutting down engine
[April 27, 2020 12:53:49 PM EDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 9.23 minutes.
Runtime.totalMemory()=2722627584
java.nio.BufferUnderflowException
at java.nio.Buffer.nextGetIndex(Buffer.java:506)
at java.nio.DirectByteBuffer.getInt(DirectByteBuffer.java:681)
at htsjdk.samtools.AbstractBAMFileIndex$MemoryMappedFileBuffer.readInteger(AbstractBAMFileIndex.java:498)
at htsjdk.samtools.AbstractBAMFileIndex.readInteger(AbstractBAMFileIndex.java:442)
at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:279)
at htsjdk.samtools.CachingBAMFileIndex.getQueryResults(CachingBAMFileIndex.java:159)
at htsjdk.samtools.CachingBAMFileIndex.getSpanOverlapping(CachingBAMFileIndex.java:70)
at htsjdk.samtools.BAMFileReader.getFileSpan(BAMFileReader.java:907)
at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:924)
at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:584)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:125)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:66)
at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:404)
at org.broadinstitute.hellbender.engine.ReadsDataSource.iterator(ReadsDataSource.java:330)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:109)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:282)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)