21:24:40 [INFO ]  Resuming from step callReditools...
21:25:05 [INFO ]  ===> fastq-dump
21:25:06 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
21:25:08 [INFO ]  ===> samtools
21:25:08 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
21:25:10 [INFO ]  ===> ../tools/FastQC/fastqc
21:25:11 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
21:25:13 [INFO ]  ===> bcftools
21:25:13 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
21:25:14 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
21:25:15 [INFO ]  ===> ../tools/hisat2-2.1.0/hisat2 --version
21:25:16 [INFO ]  Running step callReditools...
21:25:16 [INFO ]  ===> cp ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/
21:25:16 [INFO ]  Building Samtools index file for mycobacteriumTuberculosis...
21:25:16 [INFO ]  Samtools index for mycobacteriumTuberculosis already built.
21:25:16 [INFO ]  Running SNV calling with Reditools2: SRR25792492 vs mycobacteriumTuberculosis...
21:25:16 [INFO ]  ===> Job 97364: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam
21:25:16 [INFO ]  Running SNV calling with Reditools2: SRR25792493 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97365: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25792494 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97366: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25792495 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97367: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25787973 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97368: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25787974 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97369: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25787975 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97370: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25787976 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97371: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam
21:25:17 [INFO ]  Running SNV calling with Reditools2: SRR25787977 vs mycobacteriumTuberculosis...
21:25:17 [INFO ]  ===> Job 97372: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam
21:25:58 [INFO ]  ===> Job 97373: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792492.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792492.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97374: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792493.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792493.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97375: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792494.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792494.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97376: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792495.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792495.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97377: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787973.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787973.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97378: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787974.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787974.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97379: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787975.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787975.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97380: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787976.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787976.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10 
21:25:58 [INFO ]  ===> Job 97381: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787977.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787977.reditools.txt -q 25 -bq 35   -S -s 0 -os 4 -mbp 10 -Mbp 10