15:47:05 [INFO ]  Resuming from step runSnpEff...
15:47:05 [INFO ]  ===> cp ../sampleData/pathogenRef/influenzaA/influenzaA/genes.gbk ../influenzaA/data/influenzaA/genes.gbk
15:47:05 [INFO ]  ===> cp ../sampleData/pathogenRef/influenzaA/influenzaA/protein.fa ../influenzaA/data/influenzaA/protein.fa
15:47:08 [INFO ]  ===> fastq-dump
15:47:08 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
15:47:08 [INFO ]  ===> samtools
15:47:08 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
15:47:09 [INFO ]  ===> ../tools/FastQC/fastqc
15:47:09 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
15:47:10 [INFO ]  ===> bcftools
15:47:10 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
15:47:10 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
15:47:12 [INFO ]  ===> STAR
15:47:12 [INFO ]  Running step runSnpEff...
15:47:12 [INFO ]  ===> cp ../tools/snpEff/snpEff.config ../influenzaA/
15:47:12 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA
15:47:15 [INFO ]  ===> Job 96115: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051417.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051417.snpeff.reditools.vcf
15:47:15 [INFO ]  ===> Job 96116: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051417.snpeff.jacusa.vcf
15:47:15 [INFO ]  ===> Job 96117: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051423.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051423.snpeff.reditools.vcf
15:47:15 [INFO ]  ===> Job 96118: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051423.snpeff.jacusa.vcf
15:47:15 [INFO ]  ===> Job 96119: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051428.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051428.snpeff.reditools.vcf
15:47:15 [INFO ]  ===> Job 96120: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051428.snpeff.jacusa.vcf
15:47:15 [INFO ]  ===> Job 96121: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051431.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051431.snpeff.reditools.vcf
15:47:15 [INFO ]  ===> Job 96122: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051431.snpeff.jacusa.vcf
15:47:15 [INFO ]  ===> Job 96123: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051442.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051442.snpeff.reditools.vcf
15:47:15 [INFO ]  ===> Job 96124: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051442.snpeff.jacusa.vcf
15:47:15 [INFO ]  ===> Job 96125: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051450.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051450.snpeff.reditools.vcf
15:47:15 [INFO ]  ===> Job 96126: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051450.snpeff.jacusa.vcf
15:47:26 [INFO ]  Running step mergeCalling...
15:47:26 [INFO ]  Analyzing calling results from DRR051417 vs influenzaA...