15:47:59 [INFO ]  Resuming from step runSnpEff...
15:48:03 [INFO ]  ===> fastq-dump
15:48:03 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
15:48:03 [INFO ]  ===> samtools
15:48:03 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
15:48:04 [INFO ]  ===> ../tools/FastQC/fastqc
15:48:04 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
15:48:05 [INFO ]  ===> bcftools
15:48:05 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
15:48:05 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
15:48:06 [INFO ]  ===> STAR
15:48:06 [INFO ]  Running step runSnpEff...
15:48:06 [INFO ]  ===> cp ../tools/snpEff/snpEff.config ../influenzaA/
15:48:06 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA
15:48:09 [INFO ]  ===> Job 96127: ../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
15:48:09 [INFO ]  ===> Job 96128: ../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
15:48:09 [INFO ]  ===> Job 96129: ../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
15:48:09 [INFO ]  ===> Job 96130: ../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
15:48:09 [INFO ]  ===> Job 96131: ../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
15:48:09 [INFO ]  ===> Job 96132: ../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
15:48:09 [INFO ]  ===> Job 96133: ../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
15:48:09 [INFO ]  ===> Job 96134: ../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
15:48:09 [INFO ]  ===> Job 96135: ../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
15:48:09 [INFO ]  ===> Job 96136: ../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
15:48:09 [INFO ]  ===> Job 96137: ../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
15:48:09 [INFO ]  ===> Job 96138: ../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
15:48:20 [INFO ]  Running step mergeCalling...
15:48:20 [INFO ]  Analyzing calling results from DRR051417 vs influenzaA...
15:48:22 [INFO ]  Analyzing calling results from DRR051423 vs influenzaA...
15:48:23 [INFO ]  Analyzing calling results from DRR051428 vs influenzaA...
15:48:24 [INFO ]  Analyzing calling results from DRR051431 vs influenzaA...
15:48:26 [INFO ]  Analyzing calling results from DRR051442 vs influenzaA...
15:48:27 [INFO ]  Analyzing calling results from DRR051450 vs influenzaA...
15:48:27 [INFO ]  2323 positions were found.
15:48:27 [INFO ]  Generating global files...
15:48:28 [INFO ]  Generating graphs...
15:48:28 [INFO ]  Generating graphs for DRR051417 vs influenzaA...
15:48:55 [INFO ]  Generating graphs for DRR051423 vs influenzaA...
15:49:19 [INFO ]  Generating graphs for DRR051428 vs influenzaA...
15:49:45 [INFO ]  Generating graphs for DRR051431 vs influenzaA...
15:50:11 [INFO ]  Generating graphs for DRR051442 vs influenzaA...
15:50:37 [INFO ]  Generating graphs for DRR051450 vs influenzaA...
15:51:02 [INFO ]  Generating global graphs for influenzaA...
15:51:41 [INFO ]  Generating analysis report...