HaplotypeCaller does not work
Answered
REQUIRED for all errors and issues:
Due to MODULEPATH changes, the following have been reloaded:
1) ImageMagick/7 7) gnuplot/4 13) pcre/8.38 19) tidyp/1.04
2) R/3.4.2 8) gsl/2.3 14) perl/5.20.1 20) xz/5.2.3
3) autoconf/2.69 9) htslib/1.8 15) picard-tools/2.26.2 21) zlib/1.2.11
4) bzip2/1.0.6 10) java/8 16) rhel6libs/1.0
5) curl/7.46.0 11) libdeflate/0.8 17) tcl/8.6.1
6) expat/2.1.0 12) m4/1.4.17 18) texlive/2018
This software stack is maintained by the Purdue Bioinformatics Core. Please
direct inquiries regarding Bioinformatics software to bioinformatics@purdue.edu
Due to MODULEPATH changes, the following have been reloaded:
1) ImageMagick/7 7) gnuplot/4 13) pcre/8.38 19) tidyp/1.04
2) R/3.4.2 8) gsl/2.3 14) perl/5.20.1 20) xz/5.2.3
3) autoconf/2.69 9) htslib/1.8 15) picard-tools/2.26.2 21) zlib/1.2.11
4) bzip2/1.0.6 10) java/8 16) rhel6libs/1.0
5) curl/7.46.0 11) libdeflate/0.8 17) tcl/8.6.1
6) expat/2.1.0 12) m4/1.4.17 18) texlive/2018
22:08:34.532 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/depot/bioinfo/apps/apps/GATK-4.1.6.0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Oct 04, 2022 10:08:34 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
22:08:34.794 INFO HaplotypeCaller - ------------------------------------------------------------
22:08:34.795 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.6.0
22:08:34.795 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
22:08:34.795 INFO HaplotypeCaller - Executing as aebrahi@brown-a002.rcac.purdue.edu on Linux v3.10.0-1062.9.1.el7.x86_64 amd64
22:08:34.795 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-b08
22:08:34.796 INFO HaplotypeCaller - Start Date/Time: October 4, 2022 10:08:34 PM EDT
22:08:34.796 INFO HaplotypeCaller - ------------------------------------------------------------
22:08:34.797 INFO HaplotypeCaller - ------------------------------------------------------------
22:08:34.797 INFO HaplotypeCaller - HTSJDK Version: 2.21.2
22:08:34.798 INFO HaplotypeCaller - Picard Version: 2.21.9
22:08:34.798 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:08:34.798 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:08:34.798 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:08:34.798 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:08:34.798 INFO HaplotypeCaller - Deflater: IntelDeflater
22:08:34.798 INFO HaplotypeCaller - Inflater: IntelInflater
22:08:34.798 INFO HaplotypeCaller - GCS max retries/reopens: 20
22:08:34.799 INFO HaplotypeCaller - Requester pays: disabled
22:08:34.799 INFO HaplotypeCaller - Initializing engine
22:08:42.456 INFO IntervalArgumentCollection - Processing 28841373 bp from intervals
22:08:42.462 INFO HaplotypeCaller - Done initializing engine
22:08:42.471 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:08:42.482 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/depot/bioinfo/apps/apps/GATK-4.1.6.0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
22:08:42.491 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/depot/bioinfo/apps/apps/GATK-4.1.6.0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
22:08:42.537 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:08:42.537 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:08:42.537 INFO IntelPairHmm - Available threads: 4
22:08:42.537 INFO IntelPairHmm - Requested threads: 4
22:08:42.537 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:08:42.560 INFO ProgressMeter - Starting traversal
22:08:42.560 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:08:55.147 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
22:08:55.148 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
22:08:55.150 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
22:08:55.150 INFO HaplotypeCaller - Shutting down engine
[October 4, 2022 10:08:55 PM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.34 minutes.
Runtime.totalMemory()=373817344
htsjdk.samtools.util.RuntimeIOException: /scratch/brown/aebrahi/regia_ref2/all_bam/Jola-4344_aligned_dedup.bam has invalid uncompressedLength: -626257074
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:543)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:380)
at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:1022)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:840)
at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:1008)
at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:955)
at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:612)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:405)
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:416)
at org.broadinstitute.hellbender.engine.ReadsDataSource.iterator(ReadsDataSource.java:342)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:86)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:188)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
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:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
Using GATK jar /depot/bioinfo/apps/apps/GATK-4.1.6.0/gatk-package-4.1.6.0-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 -Xmx24g -jar /depot/bioinfo/apps/apps/GATK-4.1.6.0/gatk-package-4.1.6.0-local.jar HaplotypeCaller --reference persian_walnut_junglans_regia_chrs_sept18.fasta --input 3R1N_aligned_dedup.bam --input Ailantifolia_aligned_dedup.bam --input Behr_aligned_dedup.bam --input Buart_aligned_dedup.bam --input CC_aligned_dedup.bam --input CH_aligned_dedup.bam --input chandler_aligned_dedup.bam --input CI_aligned_dedup.bam --input Cinerea_aligned_dedup.bam --input CK_aligned_dedup.bam --input CP_aligned_dedup.bam --input CS_aligned_dedup.bam --input Cyc-pal_aligned_dedup.bam --input ER_aligned_dedup.bam --input Intermedia_aligned_dedup.bam --input Ja-4262_aligned_dedup.bam --input jai1_aligned_dedup.bam --input jai2_aligned_dedup.bam --input jai3_aligned_dedup.bam --input Jai-GQG24_aligned_dedup.bam --input Jai-Japan19_aligned_dedup.bam --input JCA_aligned_dedup.bam --input jcal_aligned_dedup.bam --input jcat1_aligned_dedup.bam --input jcat2_aligned_dedup.bam --input jcat3_aligned_dedup.bam --input Jcat-DZ38_aligned_dedup.bam --input Jcat-JFS18_aligned_dedup.bam --input Jcat-LQ4_aligned_dedup.bam --input Jcat-TM8_aligned_dedup.bam --input Jcat-TW219_aligned_dedup.bam --input Jcat-WLG30_aligned_dedup.bam --input Jcat-ZM7_aligned_dedup.bam --input Jcat-ZYS15_aligned_dedup.bam --input Jci-1288_aligned_dedup.bam --input Jci-1351_aligned_dedup.bam --input Jci-1378_aligned_dedup.bam --input Jci-1401_aligned_dedup.bam --input Jci-1417_aligned_dedup.bam --input Jci-1426_aligned_dedup.bam --input Jci-1445_aligned_dedup.bam --input Jci-1463_aligned_dedup.bam --input jci1_aligned_dedup.bam --input jci2_aligned_dedup.bam --input jci3_aligned_dedup.bam --input jci4_aligned_dedup.bam --input JG0001_aligned_dedup.bam --input JG0002_aligned_dedup.bam --input JG0014_aligned_dedup.bam --input JG0018_aligned_dedup.bam --input JG0026_aligned_dedup.bam --input JG0031_aligned_dedup.bam --input JG0032_aligned_dedup.bam --input JG0050_aligned_dedup.bam --input JG0051_aligned_dedup.bam --input JG0061_aligned_dedup.bam --input JG0071_aligned_dedup.bam --input JG0072_aligned_dedup.bam --input JG0166_aligned_dedup.bam --input JG0169_aligned_dedup.bam --input JG0171_aligned_dedup.bam --input JG0172_aligned_dedup.bam --input JG0173_aligned_dedup.bam --input JG0175_aligned_dedup.bam --input JG0176_aligned_dedup.bam --input JG0182_aligned_dedup.bam --input JG0184_aligned_dedup.bam --input JH_aligned_dedup.bam --input jhi_aligned_dedup.bam --input JHIN01_aligned_dedup.bam --input JHIN02_aligned_dedup.bam --input JHIN03_aligned_dedup.bam --input JHIN04_aligned_dedup.bam --input JHIN05_aligned_dedup.bam --input JHIN07_aligned_dedup.bam --input JHIN08_aligned_dedup.bam --input JHIN09_aligned_dedup.bam --input JHIN10_aligned_dedup.bam --input JHIN11_aligned_dedup.bam --input Jmad-AS4_aligned_dedup.bam --input Jmad-AT12_aligned_dedup.bam --input Jmad-CF2_aligned_dedup.bam --input Jmad-TL21_aligned_dedup.bam --input Jmad-WLS4_aligned_dedup.bam --input Jmad-XYS5_aligned_dedup.bam --input jmaj1_aligned_dedup.bam --input JM_aligned_dedup.bam --input jman1_aligned_dedup.bam --input jman2_aligned_dedup.bam --input jman3_aligned_dedup.bam --input jmi1_aligned_dedup.bam --input jmi2_aligned_dedup.bam --input jmi3_aligned_dedup.bam --input JMIC01_aligned_dedup.bam --input JMIC03_aligned_dedup.bam --input JMIC04_aligned_dedup.bam --input JMIC05_aligned_dedup.bam --input JMIC06_aligned_dedup.bam --input JMIC07_aligned_dedup.bam --input JMIC08_aligned_dedup.bam --input JMIC09_aligned_dedup.bam --input JMIC10_aligned_dedup.bam --input JMIC11_aligned_dedup.bam --input JMIC12_aligned_dedup.bam --input Jmol-4392_aligned_dedup.bam --input Jne-4244_aligned_dedup.bam --input Jne-4255_aligned_dedup.bam --input Jni-1405_aligned_dedup.bam --input Jni-1427_aligned_dedup.bam --input Jni-1438_aligned_dedup.bam --input Jni-1442_aligned_dedup.bam --input Jni-1449_aligned_dedup.bam --input Jni-1459_aligned_dedup.bam --input Jni-1465_aligned_dedup.bam --input Jni-1467_aligned_dedup.bam --input Jni-1476_aligned_dedup.bam --input jni1_aligned_dedup.bam --input jni2_aligned_dedup.bam --input jni3_aligned_dedup.bam --input jni4_aligned_dedup.bam --input Jni-Florida_aligned_dedup.bam --input JNIG01_aligned_dedup.bam --input JNIG03_aligned_dedup.bam --input JNIG04_aligned_dedup.bam --input JNIG05_aligned_dedup.bam --input JNIG07_aligned_dedup.bam --input JNIG09_aligned_dedup.bam --input JNIG10_aligned_dedup.bam --input JNIG11_aligned_dedup.bam --input JNIG12_aligned_dedup.bam --input JNIG13_aligned_dedup.bam --input JNIG14_aligned_dedup.bam --input Jola-4344_aligned_dedup.bam --input Jola-4363_aligned_dedup.bam --input Jpy-4435_aligned_dedup.bam --input JR_aligned_dedup.bam --input jre1_aligned_dedup.bam --input jre2_aligned_dedup.bam --input jre3_aligned_dedup.bam --input jre4_aligned_dedup.bam --input Jregia1_aligned_dedup.bam --input Jregia2_aligned_dedup.bam --input Jre-GX15_aligned_dedup.bam --input Jre-Y14_aligned_dedup.bam --input JS_aligned_dedup.bam --input jsi1_aligned_dedup.bam --input jsi2_aligned_dedup.bam --input jsi3_aligned_dedup.bam --input jsi4_aligned_dedup.bam --input jsi5_aligned_dedup.bam --input jsi6_aligned_dedup.bam --input Jsta-4445_aligned_dedup.bam --input Jstey-4358_aligned_dedup.bam --input Jven-4234_aligned_dedup.bam --input Major_aligned_dedup.bam --input Mand_aligned_dedup.bam --input P1_aligned_dedup.bam --input PH_aligned_dedup.bam --input PI_aligned_dedup.bam --input Plst-str_aligned_dedup.bam --input PSTE_aligned_dedup.bam --input PSTR_aligned_dedup.bam --input Pte-ste_aligned_dedup.bam --input RC_aligned_dedup.bam --input SOLEZE_aligned_dedup.bam -L Chr14 --output WG.Chr14.vcf
a) GATK version used: The Genome Analysis Toolkit (GATK) v4.1.6.0
b) Exact command used:
#!/bin/bash
#SBATCH -A woeste
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --time=330:00:00
#SBATCH --job-name=GATK
cd $SLURM_O_WORKDIR
cd /scratch/brown/aebrahi/regia_ref2/all_bam
module use /apps/group/bioinformatics/modules
module load bioinfo
module load GATK/4.1.6.0
module load samtools
module load picard-tools
#PicardCommandLine CreateSequenceDictionary R=persian_walnut_junglans_regia_chrs_sept18.fasta Output=persian_walnut_junglans_regia_chrs_sept18.dict
#java jvm-args -jar picard.jar CreateSequenceDictionary R=persian_walnut_junglans_regia_chrs_sept18.fasta Output=persian_walnut_junglans_regia_chrs_sept18.dict
#samtools faidx persian_walnut_junglans_regia_chrs_sept18.fasta
gatk --java-options "-Xmx24g" HaplotypeCaller --reference persian_walnut_junglans_regia_chrs_sept18.fasta \
--input 3R1N_aligned_dedup.bam \
--input Ailantifolia_aligned_dedup.bam \
--input Behr_aligned_dedup.bam \
--input Buart_aligned_dedup.bam \
--input CC_aligned_dedup.bam \
--input CH_aligned_dedup.bam \
--input chandler_aligned_dedup.bam \
--input CI_aligned_dedup.bam \
--input Cinerea_aligned_dedup.bam \
--input CK_aligned_dedup.bam \
--input CP_aligned_dedup.bam \
--input CS_aligned_dedup.bam \
--input Cyc-pal_aligned_dedup.bam \
--input ER_aligned_dedup.bam \
--input Intermedia_aligned_dedup.bam \
--input Ja-4262_aligned_dedup.bam \
--input jai1_aligned_dedup.bam \
--input jai2_aligned_dedup.bam \
--input jai3_aligned_dedup.bam \
--input Jai-GQG24_aligned_dedup.bam \
--input Jai-Japan19_aligned_dedup.bam \
--input JCA_aligned_dedup.bam \
--input jcal_aligned_dedup.bam \
--input jcat1_aligned_dedup.bam \
--input jcat2_aligned_dedup.bam \
--input jcat3_aligned_dedup.bam \
--input Jcat-DZ38_aligned_dedup.bam \
--input Jcat-JFS18_aligned_dedup.bam \
--input Jcat-LQ4_aligned_dedup.bam \
--input Jcat-TM8_aligned_dedup.bam \
--input Jcat-TW219_aligned_dedup.bam \
--input Jcat-WLG30_aligned_dedup.bam \
--input Jcat-ZM7_aligned_dedup.bam \
--input Jcat-ZYS15_aligned_dedup.bam \
--input Jci-1288_aligned_dedup.bam \
--input Jci-1351_aligned_dedup.bam \
--input Jci-1378_aligned_dedup.bam \
--input Jci-1401_aligned_dedup.bam \
--input Jci-1417_aligned_dedup.bam \
--input Jci-1426_aligned_dedup.bam \
--input Jci-1445_aligned_dedup.bam \
--input Jci-1463_aligned_dedup.bam \
--input jci1_aligned_dedup.bam \
--input jci2_aligned_dedup.bam \
--input jci3_aligned_dedup.bam \
--input jci4_aligned_dedup.bam \
--input JG0001_aligned_dedup.bam \
--input JG0002_aligned_dedup.bam \
--input JG0014_aligned_dedup.bam \
--input JG0018_aligned_dedup.bam \
--input JG0026_aligned_dedup.bam \
--input JG0031_aligned_dedup.bam \
--input JG0032_aligned_dedup.bam \
--input JG0050_aligned_dedup.bam \
--input JG0051_aligned_dedup.bam \
--input JG0061_aligned_dedup.bam \
--input JG0071_aligned_dedup.bam \
--input JG0072_aligned_dedup.bam \
--input JG0166_aligned_dedup.bam \
--input JG0169_aligned_dedup.bam \
--input JG0171_aligned_dedup.bam \
--input JG0172_aligned_dedup.bam \
--input JG0173_aligned_dedup.bam \
--input JG0175_aligned_dedup.bam \
--input JG0176_aligned_dedup.bam \
--input JG0182_aligned_dedup.bam \
--input JG0184_aligned_dedup.bam \
--input JH_aligned_dedup.bam \
--input jhi_aligned_dedup.bam \
--input JHIN01_aligned_dedup.bam \
--input JHIN02_aligned_dedup.bam \
--input JHIN03_aligned_dedup.bam \
--input JHIN04_aligned_dedup.bam \
--input JHIN05_aligned_dedup.bam \
--input JHIN07_aligned_dedup.bam \
--input JHIN08_aligned_dedup.bam \
--input JHIN09_aligned_dedup.bam \
--input JHIN10_aligned_dedup.bam \
--input JHIN11_aligned_dedup.bam \
--input Jmad-AS4_aligned_dedup.bam \
--input Jmad-AT12_aligned_dedup.bam \
--input Jmad-CF2_aligned_dedup.bam \
--input Jmad-TL21_aligned_dedup.bam \
--input Jmad-WLS4_aligned_dedup.bam \
--input Jmad-XYS5_aligned_dedup.bam \
--input jmaj1_aligned_dedup.bam \
--input JM_aligned_dedup.bam \
--input jman1_aligned_dedup.bam \
--input jman2_aligned_dedup.bam \
--input jman3_aligned_dedup.bam \
--input jmi1_aligned_dedup.bam \
--input jmi2_aligned_dedup.bam \
--input jmi3_aligned_dedup.bam \
--input JMIC01_aligned_dedup.bam \
--input JMIC03_aligned_dedup.bam \
--input JMIC04_aligned_dedup.bam \
--input JMIC05_aligned_dedup.bam \
--input JMIC06_aligned_dedup.bam \
--input JMIC07_aligned_dedup.bam \
--input JMIC08_aligned_dedup.bam \
--input JMIC09_aligned_dedup.bam \
--input JMIC10_aligned_dedup.bam \
--input JMIC11_aligned_dedup.bam \
--input JMIC12_aligned_dedup.bam \
--input Jmol-4392_aligned_dedup.bam \
--input Jne-4244_aligned_dedup.bam \
--input Jne-4255_aligned_dedup.bam \
--input Jni-1405_aligned_dedup.bam \
--input Jni-1427_aligned_dedup.bam \
--input Jni-1438_aligned_dedup.bam \
--input Jni-1442_aligned_dedup.bam \
--input Jni-1449_aligned_dedup.bam \
--input Jni-1459_aligned_dedup.bam \
--input Jni-1465_aligned_dedup.bam \
--input Jni-1467_aligned_dedup.bam \
--input Jni-1476_aligned_dedup.bam \
--input jni1_aligned_dedup.bam \
--input jni2_aligned_dedup.bam \
--input jni3_aligned_dedup.bam \
--input jni4_aligned_dedup.bam \
--input Jni-Florida_aligned_dedup.bam \
--input JNIG01_aligned_dedup.bam \
--input JNIG03_aligned_dedup.bam \
--input JNIG04_aligned_dedup.bam \
--input JNIG05_aligned_dedup.bam \
--input JNIG07_aligned_dedup.bam \
--input JNIG09_aligned_dedup.bam \
--input JNIG10_aligned_dedup.bam \
--input JNIG11_aligned_dedup.bam \
--input JNIG12_aligned_dedup.bam \
--input JNIG13_aligned_dedup.bam \
--input JNIG14_aligned_dedup.bam \
--input Jola-4344_aligned_dedup.bam \
--input Jola-4363_aligned_dedup.bam \
--input Jpy-4435_aligned_dedup.bam \
--input JR_aligned_dedup.bam \
--input jre1_aligned_dedup.bam \
--input jre2_aligned_dedup.bam \
--input jre3_aligned_dedup.bam \
--input jre4_aligned_dedup.bam \
--input Jregia1_aligned_dedup.bam \
--input Jregia2_aligned_dedup.bam \
--input Jre-GX15_aligned_dedup.bam \
--input Jre-Y14_aligned_dedup.bam \
--input JS_aligned_dedup.bam \
--input jsi1_aligned_dedup.bam \
--input jsi2_aligned_dedup.bam \
--input jsi3_aligned_dedup.bam \
--input jsi4_aligned_dedup.bam \
--input jsi5_aligned_dedup.bam \
--input jsi6_aligned_dedup.bam \
--input Jsta-4445_aligned_dedup.bam \
--input Jstey-4358_aligned_dedup.bam \
--input Jven-4234_aligned_dedup.bam \
--input Major_aligned_dedup.bam \
--input Mand_aligned_dedup.bam \
--input P1_aligned_dedup.bam \
--input PH_aligned_dedup.bam \
--input PI_aligned_dedup.bam \
--input Plst-str_aligned_dedup.bam \
--input PSTE_aligned_dedup.bam \
--input PSTR_aligned_dedup.bam \
--input Pte-ste_aligned_dedup.bam \
--input RC_aligned_dedup.bam \
--input SOLEZE_aligned_dedup.bam -L Chr14 --output WG.Chr14.vcf
c) Entire program log:
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Hi Aziz,
Thank you for writing into the GATK forum! It looks like there is an issue in one of your bam inputs:
/scratch/brown/aebrahi/regia_ref2/all_bam/Jola-4344_aligned_dedup.bam has invalid uncompressedLength: -626257074
You can use the tool ValidateSamFile to check for issues with this bam file and then correct the file for any problems before running HaplotypeCaller. Here is an article of what to look for: https://gatk.broadinstitute.org/hc/en-us/articles/360035891231-Errors-in-SAM-or-BAM-files-can-be-diagnosed-with-ValidateSamFile.
I would also recommend updating your GATK version just in case this is related to a bug.
Let me know how that goes for you!
Best,
Genevieve
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Hi Aziz,
We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!
Kind regards,
Genevieve
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