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WGLab / SeqMule

Automated human exome/genome variants detection from FASTQ files
http://seqmule.usc.edu
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issues about gatk when running SeqMule #169

Open gangcai opened 6 years ago

gangcai commented 6 years ago

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 commented 6 years ago

Hi

Could you post the first few (say 10) variants plus the header lines (starting with #) in the vcf (/tmp/937066.1.all.q/142865129141.234536126_nofiltered.vcf)? Thanks.

On Feb 15, 2018, at 2:43 PM, Gangcai Xie notifications@github.com wrote:

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 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. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

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gangcai commented 6 years ago

This temporary file had been deleted by the system. I will resume to run wgseg.script and hope to repeat the error.

gangcai commented 6 years ago

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 commented 6 years ago

Could you rerun from the step right before all freebayes steps?

On Feb 16, 2018, at 1:35 PM, Gangcai Xie notifications@github.com wrote:

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.

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