00:27:32 [INFO ] Resuming from step callJacusa... 00:27:38 [INFO ] ===> fastq-dump 00:27:38 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 00:27:38 [INFO ] ===> samtools 00:27:38 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 00:27:39 [INFO ] ===> ../tools/FastQC/fastqc 00:27:39 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 00:27:40 [INFO ] ===> bcftools 00:27:40 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 00:27:40 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 00:27:41 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 00:27:42 [INFO ] Running step callJacusa... 00:27:42 [INFO ] ===> cp ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa ../mtuberculosis2/4-snvCalling/indices 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25792492 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97395: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25792493 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97396: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25792494 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97397: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25792495 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97398: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25787973 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97399: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25787974 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97400: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25787975 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97401: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25787976 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97402: ../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 00:27:42 [INFO ] Running SNV calling with JACUSA: SRR25787977 vs mycobacteriumTuberculosis... 00:27:42 [INFO ] ===> Job 97403: ../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 00:37:34 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf.pre 00:37:38 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.vcf.pre 00:37:38 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792493.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792493.jacusa.vcf.pre 00:37:41 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792493.jacusa.vcf.pre 00:37:41 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792494.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792494.jacusa.vcf.pre 00:37:45 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792494.jacusa.vcf.pre 00:37:45 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792495.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792495.jacusa.vcf.pre 00:37:45 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792495.jacusa.vcf.pre 00:37:45 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787973.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787973.jacusa.vcf.pre 00:37:48 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787973.jacusa.vcf.pre 00:37:48 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787974.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787974.jacusa.vcf.pre 00:37:51 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787974.jacusa.vcf.pre 00:37:51 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787975.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787975.jacusa.vcf.pre 00:37:51 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787975.jacusa.vcf.pre 00:37:51 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787976.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787976.jacusa.vcf.pre 00:37:54 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787976.jacusa.vcf.pre 00:37:54 [INFO ] ===> mv ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787977.jacusa.vcf ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787977.jacusa.vcf.pre 00:38:00 [INFO ] ===> rm ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787977.jacusa.vcf.pre 00:38:00 [INFO ] Running step filterSOR... 00:38:00 [INFO ] ===> Job 97404: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25792492.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam 00:38:00 [INFO ] ===> Job 97405: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25792493.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam 00:38:00 [INFO ] ===> Job 97406: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25792494.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam 00:38:00 [INFO ] ===> Job 97407: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25792495.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam 00:38:00 [INFO ] ===> Job 97408: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25787973.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam 00:38:00 [INFO ] ===> Job 97409: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25787974.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam 00:38:00 [INFO ] ===> Job 97410: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25787975.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam 00:38:01 [INFO ] ===> Job 97411: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25787976.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam 00:38:01 [INFO ] ===> Job 97412: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -o ../mtuberculosis2/4-snvCalling/depths/mycobacteriumTuberculosis/SRR25787977.mpileup.vcf ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam 03:45:22 [INFO ] Analyzing SRR25792492... 03:48:55 [INFO ] Analyzing SRR25792493... 03:52:25 [INFO ] Analyzing SRR25792494... 03:55:57 [INFO ] Analyzing SRR25792495... 03:59:12 [INFO ] Analyzing SRR25787973... 04:02:42 [INFO ] Analyzing SRR25787974... 04:06:13 [INFO ] Analyzing SRR25787975... 04:09:41 [INFO ] Analyzing SRR25787976... 04:13:12 [INFO ] Analyzing SRR25787977... 04:16:44 [INFO ] Running step runSnpEff... 04:16:44 [INFO ] ===> cp ../tools/snpEff/snpEff.config ../mtuberculosis2/ 04:16:45 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../mtuberculosis2/snpEff.config -v mycobacteriumTuberculosis 04:16:52 [INFO ] ===> Job 97413: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792492.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792492.snpeff.reditools.vcf 04:16:52 [INFO ] ===> Job 97414: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792492.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792492.snpeff.jacusa.vcf 04:16:52 [INFO ] ===> Job 97415: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792493.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792493.snpeff.reditools.vcf 04:16:52 [INFO ] ===> Job 97416: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792493.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792493.snpeff.jacusa.vcf 04:16:53 [INFO ] ===> Job 97417: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792494.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792494.snpeff.reditools.vcf 04:16:53 [INFO ] ===> Job 97418: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792494.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792494.snpeff.jacusa.vcf 04:16:53 [INFO ] ===> Job 97419: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792495.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792495.snpeff.reditools.vcf 04:16:53 [INFO ] ===> Job 97420: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25792495.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25792495.snpeff.jacusa.vcf 04:16:53 [INFO ] ===> Job 97421: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787973.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787973.snpeff.reditools.vcf 04:16:53 [INFO ] ===> Job 97422: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787973.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787973.snpeff.jacusa.vcf 04:16:53 [INFO ] ===> Job 97423: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787974.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787974.snpeff.reditools.vcf 04:16:53 [INFO ] ===> Job 97424: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787974.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787974.snpeff.jacusa.vcf 04:16:53 [INFO ] ===> Job 97425: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787975.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787975.snpeff.reditools.vcf 04:16:53 [INFO ] ===> Job 97426: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787975.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787975.snpeff.jacusa.vcf 04:16:53 [INFO ] ===> Job 97427: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787976.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787976.snpeff.reditools.vcf 04:16:53 [INFO ] ===> Job 97428: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787976.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787976.snpeff.jacusa.vcf 04:16:54 [INFO ] ===> Job 97429: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787977.reditools.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787977.snpeff.reditools.vcf 04:16:54 [INFO ] ===> Job 97430: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../mtuberculosis2/snpEff.config mycobacteriumTuberculosis ../mtuberculosis2/4-snvCalling/calling/jacusa/mycobacteriumTuberculosis/SRR25787977.jacusa.presnpeff.vcf > ../mtuberculosis2/5-snpeff/mycobacteriumTuberculosis/SRR25787977.snpeff.jacusa.vcf 04:19:09 [INFO ] Running step mergeCalling... 04:19:09 [INFO ] Analyzing calling results from SRR25792492 vs mycobacteriumTuberculosis... 04:23:00 [INFO ] Analyzing calling results from SRR25792493 vs mycobacteriumTuberculosis... 04:26:40 [INFO ] Analyzing calling results from SRR25792494 vs mycobacteriumTuberculosis... 04:30:29 [INFO ] Analyzing calling results from SRR25792495 vs mycobacteriumTuberculosis... 04:32:43 [INFO ] Analyzing calling results from SRR25787973 vs mycobacteriumTuberculosis... 04:36:18 [INFO ] Analyzing calling results from SRR25787974 vs mycobacteriumTuberculosis... 04:39:41 [INFO ] Analyzing calling results from SRR25787975 vs mycobacteriumTuberculosis... 04:42:20 [INFO ] Analyzing calling results from SRR25787976 vs mycobacteriumTuberculosis... 04:45:40 [INFO ] Analyzing calling results from SRR25787977 vs mycobacteriumTuberculosis... 04:51:03 [INFO ] 75070 positions were found. 04:51:03 [INFO ] Generating global files... 04:51:09 [INFO ] Generating graphs... 04:51:09 [INFO ] Generating graphs for SRR25792492 vs mycobacteriumTuberculosis... 04:53:35 [INFO ] Generating graphs for SRR25792493 vs mycobacteriumTuberculosis... 04:56:10 [INFO ] Generating graphs for SRR25792494 vs mycobacteriumTuberculosis... 04:58:31 [INFO ] Generating graphs for SRR25792495 vs mycobacteriumTuberculosis... 04:58:45 [INFO ] Generating graphs for SRR25787973 vs mycobacteriumTuberculosis... 05:00:49 [INFO ] Generating graphs for SRR25787974 vs mycobacteriumTuberculosis... 05:03:05 [INFO ] Generating graphs for SRR25787975 vs mycobacteriumTuberculosis... 05:03:48 [INFO ] Generating graphs for SRR25787976 vs mycobacteriumTuberculosis... 05:05:28 [INFO ] Generating graphs for SRR25787977 vs mycobacteriumTuberculosis... 05:10:11 [INFO ] Generating global graphs for mycobacteriumTuberculosis... 05:10:12 [INFO ] Generating analysis report...