Run example fastq files with error

[DecodeGenome]

Hi Yunfei,

I newly installed SeqMule (SeqMule-master) on CentOS, seqmule download the database, and ran the example command with example fastq files, I got error, how to fix it? Thanks for your help. WEI
############################################################################################
java -Xmx1750m -Djava.io.tmpdir=/scratch/wwu888 -jar /wynton/group/bivona/Analytic_tools/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -T IndelRealigner -I example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -R /wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta -targetIntervals /scratch/wwu888/8505.50003740059.tmp.intervals --out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam -maxInMemory 200000 -L /wynton/group/bivona/Analytic_tools/SeqMule-master/misc/hg19_exonPlus5bp_UCSCrefGene.bed -rf NotPrimaryAlignment -l ERROR
rm -rf /scratch/wwu888/8505.50003740059.tmp.intervals
/wynton/group/bivona/Analytic_tools/SeqMule-master/exe/samtools/samtools index example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam at /wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN line 78.

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----------
[ => SeqMule Execution Status: step 7 FAILED at Tue May 3 20:13:10 PDT 2022, gatklite realn]
ERROR: command failed
/wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../bin/secondary/worker /wynton/group/bivona/Data/Seqmule_Test_fq_May3_2022/seqmule.05032022.10358.logs 7 "/wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced example.config -n 6 -ref /wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta -java java -jmem 1750m -gatk /wynton/group/bivona/Analytic_tools/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /scratch/wwu888 -bed /wynton/group/bivona/Analytic_tools/SeqMule-master/misc/hg19_exonPlus5bp_UCSCrefGene.bed -goldindel /wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf -dbsnp /wynton/group/bivona/Analytic_tools/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf -samtools /wynton/group/bivona/Analytic_tools/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /wynton/group/bivona/Data/Seqmule_Test_fq_May3_2022' and 'seqmule run example.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

[yunfeiguo]

Hi @DecodeGenome what's your java version (java -version)? This issue might be caused by the main problem as in #186

[DecodeGenome]

Hi Yunfei: thanks for your response, below is the java version on HPC dev node:
Thanks
Wei
###############
(base) [wwu888@dev3 ~]$ java -version
openjdk version "1.8.0_322"
OpenJDK Runtime Environment (build 1.8.0_322-b06)
OpenJDK 64-Bit Server VM (build 25.322-b06, mixed mode)

[yunfeiguo]

Can you try Oracle jdk8? The NullPointer exception is clueless to me otherwise. You can also try dockerized seqmule (https://hub.docker.com/layers/seqmule/genomicslab/seqmule/latest/images/sha256-09d8c5458f956cf6e7213a90b14657e0fea68d84e6a812f4100199f99cf5272f?context=explore).

…

________________________________ 发件人: DecodeGenome ***@***.***> 发送时间: Wednesday, May 4, 2022 9:34:51 PM 收件人: WGLab/SeqMule ***@***.***> 抄送: Yunfei Guo ***@***.***>; Comment ***@***.***> 主题: Re: [WGLab/SeqMule] Run example fastq files with error (Issue #187) Hi Yunfei: thanks for your response, below is the java version on HPC dev node: Thanks Wei ############### (base) ***@***.*** ~]$ java -version openjdk version "1.8.0_322" OpenJDK Runtime Environment (build 1.8.0_322-b06) OpenJDK 64-Bit Server VM (build 25.322-b06, mixed mode) ― Reply to this email directly, view it on GitHub<#187 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB3A7TVOK55QLKNO7GD7X5LVIMQTXANCNFSM5VAXYUMQ>. You are receiving this because you commented.Message ID: ***@***.***>

[DecodeGenome]

Thank you YUNFEI, I may try to use dockerized seqmule as you suggest.

[DecodeGenome]

Hi Yunfei, I have pulled genomiclab/seqmule image, I tried to run "docker run -it genomiclab/seqmule pipeline " it does not work. since I am not familiar too much with docker, do you have detailed instructions to use docker for seqmule?

Thanks,

Wei

[yunfeiguo]

Hi @DecodeGenome please try the following command as dockerized quick start in tutorial (https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/Tutorials/Quick%20start/)

docker run -v $(pwd):/input -v $(pwd)/output:/opt/app-root/src -it genomicslab/seqmule /opt/SeqMule/bin/seqmule pipeline -a /root/normal_R1.fastq.gz -b /root/normal_R2.fastq.gz -prefix example -N 2 -capture default -threads 4 -e

assuming you have normal_R1.fastq.gz and normal_R2.fastq.gz in your current working directory plus an output folder. The /opt/app-root/src path is the default working directory after logging into docker container and is used for storing output files.