00:19:46 [INFO ]  Resuming from step callReditools...
00:19:59 [INFO ]  ===> fastq-dump
00:20:00 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
00:20:01 [INFO ]  ===> samtools
00:20:01 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
00:20:04 [INFO ]  ===> ../tools/FastQC/fastqc
00:20:05 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
00:20:06 [INFO ]  ===> bcftools
00:20:06 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
00:20:06 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
00:20:09 [INFO ]  ===> ../tools/hisat2-2.1.0/hisat2 --version
00:20:10 [INFO ]  Running step callReditools...
00:20:10 [INFO ]  ===> cp ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/
00:20:10 [INFO ]  Building Samtools index file for mycobacteriumTuberculosis...
00:20:10 [INFO ]  Samtools index for mycobacteriumTuberculosis already built.
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25792492 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25792493 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25792494 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25792495 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25787973 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25787974 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25787975 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25787976 vs mycobacteriumTuberculosis...
00:20:10 [INFO ]  Running SNV calling with Reditools2: SRR25787977 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  Running step callJacusa...
00:22:39 [INFO ]  ===> cp ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa ../mtuberculosis2/4-snvCalling/indices
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25792492 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97386: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25792493 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97387: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792493.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25792494 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97388: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792494.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25792495 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97389: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792495.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25787973 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97390: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787973.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25787974 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97391: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787974.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25787975 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97392: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787975.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25787976 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97393: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787976.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam
00:22:39 [INFO ]  Running SNV calling with JACUSA: SRR25787977 vs mycobacteriumTuberculosis...
00:22:39 [INFO ]  ===> Job 97394: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787977.jacusa.vcf -s -f V -m 25 -q 35   -a B,I,Y  ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam
00:22:40 [INFO ]  ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf.pre
00:22:40 [ERROR]  mv: cannot stat ‘../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf’: No such file or directory