No variant calling after alignment

[DecodeGenome]

Hi Yunfei,

SeqMule works well before, now There is an error from step 7, please help out to solve the issue. Thanks.

Wei
#######################################################################
[7]
JOBID=0
PID=60845
command=/home/wwu1/SeqMule/bin/secondary/../../bin/secondary/worker /bivonalab/data1/WW_DATA_PROCESS/WES/ALL_fastq/seqmule.05022022.10084.logs 7 "/home/wwu1/SeqMule/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced H2405.config -n 6 -ref /home/wwu1/SeqMule/bin/secondary/../../database/human_g1k_v37.fasta -java java -jmem 1750m -gatk /home/wwu1/SeqMule/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /scratch/wwu1/502533 -bed /home/wwu1/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed -goldindel /home/wwu1/SeqMule/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf -dbsnp /home/wwu1/SeqMule/bin/secondary/../../database/dbsnp_hg19_138.vcf -samtools /home/wwu1/SeqMule/exe/samtools/samtools -pl ILLUMINA -bam H2405_result/H2405.0_bwamem.sort.rmdup.readfiltered.bam -out H2405_result/H2405.0_bwamem.sort.rmdup.readfiltered.realn.bam "
dependency=6
message=gatklite realn
nCPU_requested=4
status=error
######################
----------NOTICE----------
[ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at Tue May 3 17:35:48 PDT 2022, Time Elapsed: 9 hr 47 min 7 s]
[ => SeqMule Execution Status: step 6 is finished at Tue May 3 17:35:48 PDT 2022, Filter BAM file by mapping quality]

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----------
[ => SeqMule Execution Status: step 7 FAILED at Tue May 3 17:35:51 PDT 2022, gatklite realn]
ERROR: command failed
/home/wwu1/SeqMule/bin/secondary/../../bin/secondary/worker /bivonalab/data1/WW_DATA_PROCESS/WES/ALL_fastq/seqmule.05032022.60891.logs 7 "/home/wwu1/SeqMule/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced H2405KR.config -n 6 -ref /home/wwu1/SeqMule/bin/secondary/../../database/human_g1k_v37.fasta -java java -jmem 1750m -gatk /home/wwu1/SeqMule/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /scratch/wwu1/502533 -bed /home/wwu1/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed -goldindel /home/wwu1/SeqMule/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf -dbsnp /home/wwu1/SeqMule/bin/secondary/../../database/dbsnp_hg19_138.vcf -samtools /home/wwu1/SeqMule/exe/samtools/samtools -pl ILLUMINA -bam H2405KR_result/H2405KR.0_bwamem.sort.rmdup.readfiltered.bam -out H2405KR_result/H2405KR.0_bwamem.sort.rmdup.readfiltered.realn.bam "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /bivonalab/data1/WW_DATA_PROCESS/WES/ALL_fastq' and 'seqmule run H2405KR.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!