ipstone/modules

cluster_samples fail when running mouse WES samples

ipstone opened this issue · 3 comments

ipstone commented

it fails at

Started at Sat Jan 2 13:12:09 2021
Terminated at Sat Jan 2 13:12:15 2021
Results reported at Sat Jan 2 13:12:15 2021

Exited with exit code 1.

Resource usage summary:

CPU time :                                   10.76 sec.
Max Memory :                                 1 GB
Average Memory :                             0.60 GB
Total Requested Memory :                     16.00 GB
Delta Memory :                               15.00 GB
Max Swap :                                   -    Max Processes :                              4    Max Threads :                                62
Run time :                                   6 sec.    Turnaround time :                            6 sec.

The output (if any) follows:

INFO 13:12:12,445 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:12:12,447 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-gcfc45fd, Compiled 2014/03/31 11:48:54
INFO 13:12:12,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:12:12,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:12:12,450 HelpFormatter - Program Args: -S LENIENT -T UnifiedGenotyper -nt 4 -R /home/ipstone/share/reference/Mus_musculus_GRCm38/Mus_musculus.GRCm38.71.dna.chromosome.genome.fa --dbsnp /home/ipstone/share/reference/mgp.v5.merged.snps_all.dbSNP142.vcf.gz -I bam/study-sample.bam -L /home/ipstone/share/reference/dbsnp_tseq_intersect.bed -o snp_vcf/study-sample.snps.vcf --output_mode EMIT_ALL_SITES
INFO 13:12:12,454 HelpFormatter - Executing as ipstone@lt13 on Linux 3.10.0-957.12.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18.
INFO 13:12:12,454 HelpFormatter - Date/Time: 2021/01/02 13:12:12
INFO 13:12:12,454 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:12:12,455 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:12:13,015 GenomeAnalysisEngine - Strictness is LENIENT
INFO 13:12:13,091 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 13:12:13,098 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:12:13,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
INFO 13:12:14,961 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.1-1-gcfc45fd):
ERROR##### ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ipstone commented

It seems the cluster_samples target is using the wrong dbSNPs in its code:

These are probably human snps:

ifeq ($(EXOME),true)
DBSNP_SUBSET ?= $(HOME)/share/reference/dbsnp_137_exome.bed
else
DBSNP_SUBSET = $(HOME)/share/reference/dbsnp_tseq_intersect.bed
endif

ipstone commented

Just modified the clusterSamples.mk
to

14 ifeq ($(EXOME),true)
~ 15 #DBSNP_SUBSET ?= $(HOME)/share/reference/dbsnp_137_exome.bed

  • 16 DBSNP_SUBSET ?= $(HOME)/share/reference/mus_musculus_known_genes_exons_GRCm38_noheader.bed
  • 17 # -- modified subset to the mouse exome region

Will test this out once current run is done.

ipstone commented

this modification make the cluster_samples work properly.