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GATK HaplotypeCaller stalls after initializing bam readers

JautisJautis DukeMember

Hello, I am running GATK's HaplotypeCaller on 290 bam files. GATK starts fine and finishes the step stating "Done initializing BAM readers". However, it never proceeds to outputting a vcf file and has been stuck in this state for 10+ hours.

Is this normal behavior and are there any steps you would recommend other than waiting indefinitely for this step to finish or an actual error message? These are relatively small scaffolds (only a couple megabases long). Bam files are split by scaffold, so each run of GATK is for 290 files that are 3-7 Mbs.

Thanks in advance for your help! Here is my code for running HaplotypeCaller and the output it produces; please let me know if there is anymore information which would be helpful!

code:
chrom=head -$index scaffolds.txt | tail -1 ; java -jar ./Programs/GenomeAnalysisTK.jar -T HaplotypeCaller -R $path_genome -I list.$chrom.list -o calls.raw.$chrom.vcf -stand_call_conf 20.0 -stand_emit_conf 20.0 -L $chrom

output:
INFO 16:47:19,176 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:47:19,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO 16:47:19,178 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:47:19,178 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:47:19,181 HelpFormatter - Program Args: -T HaplotypeCaller -R ./genomes/assembly.fasta -I list.scaffold5.list -o calls.raw.scaffold5.vcf -stand_call_conf 20.0 -stand_emit_conf 20.0 -L scaffold5
INFO 16:47:19,200 HelpFormatter - Executing as [email protected] on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 16:47:19,200 HelpFormatter - Date/Time: 2018/12/06 16:47:19
INFO 16:47:19,201 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:47:19,201 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:47:19,718 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:47:20,174 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 16:47:20,181 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:47:27,330 SAMDataSource$SAMReaders - Init 50 BAMs in last 7.15 s, 50 of 290 in 7.15 s / 0.12 m (7.00 tasks/s). 240 remaining with est. completion in 34.31 s / 0.57 m
INFO 16:47:33,970 SAMDataSource$SAMReaders - Init 50 BAMs in last 6.64 s, 100 of 290 in 13.79 s / 0.23 m (7.25 tasks/s). 190 remaining with est. completion in 26.20 s / 0.44 m
INFO 16:47:40,313 SAMDataSource$SAMReaders - Init 50 BAMs in last 6.34 s, 150 of 290 in 20.13 s / 0.34 m (7.45 tasks/s). 140 remaining with est. completion in 18.79 s / 0.31 m
INFO 16:47:47,006 SAMDataSource$SAMReaders - Init 50 BAMs in last 6.69 s, 200 of 290 in 26.82 s / 0.45 m (7.46 tasks/s). 90 remaining with est. completion in 12.07 s / 0.20 m
INFO 16:47:53,468 SAMDataSource$SAMReaders - Init 50 BAMs in last 6.46 s, 250 of 290 in 33.29 s / 0.55 m (7.51 tasks/s). 40 remaining with est. completion in 5.33 s / 0.09 m
INFO 16:47:56,553 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 36.37

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