04:58:28 [INFO ] Resuming from step callReditools... 04:58:47 [INFO ] ===> fastq-dump 04:58:48 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 04:58:49 [INFO ] ===> samtools 04:58:49 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 04:58:50 [INFO ] ===> ../tools/FastQC/fastqc 04:58:51 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 04:58:52 [INFO ] ===> bcftools 04:58:52 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 04:58:53 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 04:58:55 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 04:58:56 [INFO ] Running step callReditools... 04:58:56 [INFO ] ===> cp ../hcapsulatum/data/genome/genome.fa ../hcapsulatum/4-snvCalling/indices/genome/ 04:58:56 [INFO ] Building Samtools index file for genome... 04:58:56 [INFO ] ===> Job 96619: samtools faidx ../hcapsulatum/4-snvCalling/indices/genome/genome.fa > ../hcapsulatum/4-snvCalling/indices/genome/genome_faidx.done 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR950197 vs genome... 04:58:56 [INFO ] ===> Job 96620: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR950198 vs genome... 04:58:56 [INFO ] ===> Job 96621: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR949916 vs genome... 04:58:56 [INFO ] ===> Job 96622: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR950093 vs genome... 04:58:56 [INFO ] ===> Job 96623: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR949601 vs genome... 04:58:56 [INFO ] ===> Job 96624: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR949624 vs genome... 04:58:56 [INFO ] ===> Job 96625: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR949060 vs genome... 04:58:56 [INFO ] ===> Job 96626: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam 04:58:56 [INFO ] Running SNV calling with Reditools2: SRR949270 vs genome... 04:58:56 [INFO ] ===> Job 96627: samtools index ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam 04:59:10 [INFO ] ===> Job 96628: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR950197.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR950197.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:10 [INFO ] ===> Job 96629: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR950198.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR950198.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:10 [INFO ] ===> Job 96630: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR949916.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949916.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:10 [INFO ] ===> Job 96631: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR950093.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR950093.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:10 [INFO ] ===> Job 96632: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR949601.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949601.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:10 [INFO ] ===> Job 96633: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR949624.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949624.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:10 [INFO ] ===> Job 96634: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR949060.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949060.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 04:59:11 [INFO ] ===> Job 96635: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam -r ../hcapsulatum/4-snvCalling/indices/genome/genome.fa -m ../hcapsulatum/4-snvCalling/homopol/genome/SRR949270.homopol.txt -o ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949270.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 06:26:40 [INFO ] Running step callJacusa... 06:26:40 [INFO ] ===> cp ../hcapsulatum/data/genome/genome.fa ../hcapsulatum/4-snvCalling/indices 06:26:40 [INFO ] Running SNV calling with JACUSA: SRR950197 vs genome... 06:26:41 [INFO ] ===> Job 96636: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950197.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR950198 vs genome... 06:26:41 [INFO ] ===> Job 96637: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950198.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR949916 vs genome... 06:26:41 [INFO ] ===> Job 96638: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949916.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR950093 vs genome... 06:26:41 [INFO ] ===> Job 96639: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950093.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR949601 vs genome... 06:26:41 [INFO ] ===> Job 96640: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949601.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR949624 vs genome... 06:26:41 [INFO ] ===> Job 96641: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949624.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR949060 vs genome... 06:26:41 [INFO ] ===> Job 96642: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949060.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam 06:26:41 [INFO ] Running SNV calling with JACUSA: SRR949270 vs genome... 06:26:41 [INFO ] ===> Job 96643: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949270.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam 06:28:10 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950197.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950197.jacusa.vcf.pre 06:28:13 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950197.jacusa.vcf.pre 06:28:13 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950198.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950198.jacusa.vcf.pre 06:28:15 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950198.jacusa.vcf.pre 06:28:15 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949916.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949916.jacusa.vcf.pre 06:28:17 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949916.jacusa.vcf.pre 06:28:17 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950093.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950093.jacusa.vcf.pre 06:28:19 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950093.jacusa.vcf.pre 06:28:19 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949601.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949601.jacusa.vcf.pre 06:28:21 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949601.jacusa.vcf.pre 06:28:21 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949624.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949624.jacusa.vcf.pre 06:28:22 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949624.jacusa.vcf.pre 06:28:22 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949060.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949060.jacusa.vcf.pre 06:28:23 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949060.jacusa.vcf.pre 06:28:23 [INFO ] ===> mv ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949270.jacusa.vcf ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949270.jacusa.vcf.pre 06:28:24 [INFO ] ===> rm ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949270.jacusa.vcf.pre 06:28:24 [INFO ] Running step filterSOR... 06:28:24 [INFO ] ===> Job 96644: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR950197.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam 06:28:24 [INFO ] ===> Job 96645: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR950198.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam 06:28:24 [INFO ] ===> Job 96646: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR949916.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam 06:28:24 [INFO ] ===> Job 96647: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR950093.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam 06:28:24 [INFO ] ===> Job 96648: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR949601.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam 06:28:24 [INFO ] ===> Job 96649: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR949624.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam 06:28:24 [INFO ] ===> Job 96650: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR949060.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam 06:28:24 [INFO ] ===> Job 96651: bcftools mpileup -q 25 -Q 35 -A -I -d 1000000 -a FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP -O v -f ../hcapsulatum/data/genome/genome.fa -o ../hcapsulatum/4-snvCalling/depths/genome/SRR949270.mpileup.vcf ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam 06:56:46 [INFO ] Analyzing SRR950197... 07:18:21 [INFO ] Analyzing SRR950198... 07:39:58 [INFO ] Analyzing SRR949916... 08:01:53 [INFO ] Analyzing SRR950093... 08:23:45 [INFO ] Analyzing SRR949601... 08:44:43 [INFO ] Analyzing SRR949624... 09:04:42 [INFO ] Analyzing SRR949060... 09:25:49 [INFO ] Analyzing SRR949270... 09:47:10 [INFO ] Running step runSnpEff... 09:47:10 [INFO ] ===> cp ../tools/snpEff/snpEff.config ../hcapsulatum/ 09:47:11 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../hcapsulatum/snpEff.config -v genome 09:47:27 [INFO ] ===> Job 96652: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR950197.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR950197.snpeff.reditools.vcf 09:47:27 [INFO ] ===> Job 96653: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950197.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR950197.snpeff.jacusa.vcf 09:47:27 [INFO ] ===> Job 96654: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR950198.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR950198.snpeff.reditools.vcf 09:47:27 [INFO ] ===> Job 96655: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950198.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR950198.snpeff.jacusa.vcf 09:47:27 [INFO ] ===> Job 96656: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949916.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949916.snpeff.reditools.vcf 09:47:27 [INFO ] ===> Job 96657: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949916.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949916.snpeff.jacusa.vcf 09:47:27 [INFO ] ===> Job 96658: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR950093.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR950093.snpeff.reditools.vcf 09:47:27 [INFO ] ===> Job 96659: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR950093.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR950093.snpeff.jacusa.vcf 09:47:27 [INFO ] ===> Job 96660: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949601.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949601.snpeff.reditools.vcf 09:47:28 [INFO ] ===> Job 96661: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949601.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949601.snpeff.jacusa.vcf 09:47:28 [INFO ] ===> Job 96662: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949624.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949624.snpeff.reditools.vcf 09:47:28 [INFO ] ===> Job 96663: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949624.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949624.snpeff.jacusa.vcf 09:47:28 [INFO ] ===> Job 96664: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949060.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949060.snpeff.reditools.vcf 09:47:28 [INFO ] ===> Job 96665: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949060.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949060.snpeff.jacusa.vcf 09:47:28 [INFO ] ===> Job 96666: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/reditools/genome/SRR949270.reditools.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949270.snpeff.reditools.vcf 09:47:28 [INFO ] ===> Job 96667: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../hcapsulatum/snpEff.config genome ../hcapsulatum/4-snvCalling/calling/jacusa/genome/SRR949270.jacusa.presnpeff.vcf > ../hcapsulatum/5-snpeff/genome/SRR949270.snpeff.jacusa.vcf 09:48:14 [INFO ] Running step mergeCalling... 09:48:14 [INFO ] Analyzing calling results from SRR950197 vs genome... 10:03:50 [INFO ] Analyzing calling results from SRR950198 vs genome... 10:19:42 [INFO ] Analyzing calling results from SRR949916 vs genome... 10:35:25 [INFO ] Analyzing calling results from SRR950093 vs genome... 10:51:27 [INFO ] Analyzing calling results from SRR949601 vs genome... 11:06:50 [INFO ] Analyzing calling results from SRR949624 vs genome... 11:21:07 [INFO ] Analyzing calling results from SRR949060 vs genome... 11:36:00 [INFO ] Analyzing calling results from SRR949270 vs genome... 11:50:44 [INFO ] 69070 positions were found. 11:50:44 [INFO ] Generating global files... 11:50:50 [INFO ] Generating graphs... 11:50:50 [INFO ] Generating graphs for SRR950197 vs genome... 12:41:11 [INFO ] Generating graphs for SRR950198 vs genome... 13:25:15 [INFO ] Generating graphs for SRR949916 vs genome... 13:27:26 [INFO ] Generating graphs for SRR950093 vs genome... 13:29:34 [INFO ] Generating graphs for SRR949601 vs genome... 14:11:44 [INFO ] Generating graphs for SRR949624 vs genome... 14:46:41 [INFO ] Generating graphs for SRR949060 vs genome... 14:47:16 [INFO ] Generating graphs for SRR949270 vs genome... 14:47:44 [INFO ] Generating global graphs for genome...