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issues about gatk when running SeqMule #169

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gangcai opened this issue Feb 15, 2018 · 4 comments
Open

issues about gatk when running SeqMule #169

gangcai opened this issue Feb 15, 2018 · 4 comments

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@gangcai
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gangcai commented Feb 15, 2018

Hi Yunfei,
Here is an error I met during running SeqMule.
The SeqMule command is:
seqmule pipeline -a r1.fastq.gz -b r2.fastq.gz -advanced ./predefined_config/snap_freebayes.config -quick -t 6 -g -prefix wgseg

The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836

Following is the error message:
NOTICE: Counting non-empty lines in /tmp/937066.1.all.q/142865129141.234536126_nofiltered.vcf
NOTICE: 0 records removed because of being filtered.

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:160)
at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:53)
at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:54)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
Caused by: java.lang.NullPointerException
at org.reflections.Reflections.scan(Reflections.java:220)
at org.reflections.Reflections.scan(Reflections.java:166)
at org.reflections.Reflections.(Reflections.java:94)
at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:77)
... 4 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-gdcdccbb):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

ERROR: Failed to split VCF by sample
NOTICE: Cleaning...

----------ERROR----------
[ => SeqMule Execution Status: step 13 FAILED at Tue Feb 13 20:15:24 EST 2018, Merge split VCF]
ERROR: command failed
~/lab//packages/SeqMule/bin/secondary/../../bin/secondary/worker /lab//projects/WGS_Analysis/run_SeqMule/WGS/seqmule.02122018.122783.logs 13 "/lab//packages/SeqMule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp/937066.1.all.q -ref ~/lab//packages/SeqMule/bin/secondary/../../database/human_g1k_v37.fasta -jmem 1750m -jexe java -t 2 -u-vcf wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.0_freebayes.vcf,wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.1_freebayes.vcf,wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.2_freebayes.vcf,wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.3_freebayes.vcf,wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.4_freebayes.vcf,wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.5_freebayes.vcf -p wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.0_freebayes && mv -f wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.0_freebayes_union.vcf wgseg_result/wgseg.0_snap.sort.rmdup.readfiltered.0_freebayes.vcf"
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd ~/lab//projects/WGS_Analysis/run_SeqMule/WGS' and 'seqmule run wgseg.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@yunfeiguo
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yunfeiguo commented Feb 16, 2018 via email

@gangcai
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gangcai commented Feb 16, 2018 •
edited
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This temporary file had been deleted by the system. I will resume to run wgseg.script and hope to repeat the error.

@gangcai
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gangcai commented Feb 16, 2018

Here is the error message to run:
seqmule run wgseg.script

It seems that to resume to run SeqMule, it still needs those temporary files generated from last step.

Current version: 1.2.6
[ => SeqMule Execution Status: step 8 is finished at Fri Feb 16 16:01:12 EST 2018, freebayes variant calling]

[ => SeqMule Execution Status: step 9 is finished at Fri Feb 16 16:01:12 EST 2018, freebayes variant calling]

[ => SeqMule Execution Status: step 10 is finished at Fri Feb 16 16:01:12 EST 2018, freebayes variant calling]

[ => SeqMule Execution Status: step 11 is finished at Fri Feb 16 16:01:12 EST 2018, freebayes variant calling]

[ => SeqMule Execution Status: step 12 is finished at Fri Feb 16 16:01:12 EST 2018, freebayes variant calling]

Check for upgrade ...
NOTICE: This is the latest version!
sh: /tmp/937066.1.all.q/190774148494.804902188_nofiltered.vcf: No such file or directory
ERROR: Failed to extract variants that passed filtering or have no filter.

@yunfeiguo
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yunfeiguo commented Feb 16, 2018 via email

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@gangcai @yunfeiguo