13:11:22 [INFO ]  Resuming from step filterSOR...
13:11:27 [INFO ]  ===> fastq-dump
13:11:27 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
13:11:27 [INFO ]  ===> samtools
13:11:28 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
13:11:28 [INFO ]  ===> ../tools/FastQC/fastqc
13:11:29 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
13:11:29 [INFO ]  ===> bcftools
13:11:29 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
13:11:29 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
13:11:31 [INFO ]  ===> STAR
13:11:31 [INFO ]  Running step filterSOR...
13:11:31 [INFO ]  ===> Job 96073: bcftools mpileup -q 25 -Q 35   -A -I -d 1000000  -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../influenzaA/data/influenzaA/genome.fa -o ../influenzaA/4-snvCalling/depths/influenzaA/DRR051417.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.bam
13:11:31 [INFO ]  ===> Job 96074: bcftools mpileup -q 25 -Q 35   -A -I -d 1000000  -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../influenzaA/data/influenzaA/genome.fa -o ../influenzaA/4-snvCalling/depths/influenzaA/DRR051423.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.bam
13:11:31 [INFO ]  ===> Job 96075: bcftools mpileup -q 25 -Q 35   -A -I -d 1000000  -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../influenzaA/data/influenzaA/genome.fa -o ../influenzaA/4-snvCalling/depths/influenzaA/DRR051428.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.bam
13:11:31 [INFO ]  ===> Job 96076: bcftools mpileup -q 25 -Q 35   -A -I -d 1000000  -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../influenzaA/data/influenzaA/genome.fa -o ../influenzaA/4-snvCalling/depths/influenzaA/DRR051431.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.bam
13:11:31 [INFO ]  ===> Job 96077: bcftools mpileup -q 25 -Q 35   -A -I -d 1000000  -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../influenzaA/data/influenzaA/genome.fa -o ../influenzaA/4-snvCalling/depths/influenzaA/DRR051442.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.bam
13:11:31 [INFO ]  ===> Job 96078: bcftools mpileup -q 25 -Q 35   -A -I -d 1000000  -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../influenzaA/data/influenzaA/genome.fa -o ../influenzaA/4-snvCalling/depths/influenzaA/DRR051450.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.bam
13:11:46 [INFO ]  Analyzing DRR051417...
13:11:49 [INFO ]  Analyzing DRR051423...
13:11:50 [INFO ]  Analyzing DRR051428...
13:11:50 [INFO ]  Analyzing DRR051431...
13:11:51 [INFO ]  Analyzing DRR051442...
13:11:52 [INFO ]  Analyzing DRR051450...
13:11:53 [INFO ]  Running step runSnpEff...
13:11:53 [INFO ]  ===> cp ../tools/snpEff/snpEff.config ../influenzaA/
13:11:53 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA
13:11:56 [INFO ]  ===> Job 96079: ../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
13:11:56 [INFO ]  ===> Job 96080: ../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
13:11:56 [INFO ]  ===> Job 96081: ../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
13:11:56 [INFO ]  ===> Job 96082: ../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
13:11:56 [INFO ]  ===> Job 96083: ../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
13:11:56 [INFO ]  ===> Job 96084: ../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
13:11:56 [INFO ]  ===> Job 96085: ../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
13:11:56 [INFO ]  ===> Job 96086: ../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
13:11:56 [INFO ]  ===> Job 96087: ../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
13:11:56 [INFO ]  ===> Job 96088: ../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
13:11:56 [INFO ]  ===> Job 96089: ../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
13:11:56 [INFO ]  ===> Job 96090: ../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
13:12:03 [INFO ]  Running step mergeCalling...
13:12:03 [INFO ]  Analyzing calling results from DRR051417 vs influenzaA...