22:10:22 [INFO ] Resuming from step hostAlignment... 22:10:27 [INFO ] ===> fastq-dump 22:10:27 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 22:10:27 [INFO ] ===> samtools 22:10:27 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 22:10:28 [INFO ] ===> ../tools/FastQC/fastqc 22:10:28 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 22:10:29 [INFO ] ===> bcftools 22:10:29 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 22:10:29 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 22:10:30 [INFO ] ===> bwa 22:10:31 [INFO ] Running step hostAlignment... 22:10:31 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 22:10:45 [INFO ] Building BWA index file for Homo_sapiens_GRCh38... 22:10:45 [INFO ] BWA index for Homo_sapiens_GRCh38 already built. 22:10:45 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96412: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051417_1.fastq ../influenzaA/1-quality/fastq/DRR051417_2.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051417_bwa.sam 22:10:45 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96413: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051423_1.fastq ../influenzaA/1-quality/fastq/DRR051423_2.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051423_bwa.sam 22:10:45 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96414: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051428_1.fastq ../influenzaA/1-quality/fastq/DRR051428_2.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051428_bwa.sam 22:10:45 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96415: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051431_1.fastq ../influenzaA/1-quality/fastq/DRR051431_2.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051431_bwa.sam 22:10:45 [INFO ] Mapping DRR051442.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96416: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051442.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051442_bwa.sam 22:10:45 [INFO ] Mapping DRR051444.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96417: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051444.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051444_bwa.sam 22:10:45 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 22:10:45 [INFO ] ===> Job 96418: bwa mem -t 16 ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 ../influenzaA/1-quality/fastq/DRR051450_1.fastq ../influenzaA/1-quality/fastq/DRR051450_2.fastq > ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051450_bwa.sam 22:11:38 [INFO ] Running step removeAligned... 22:11:38 [INFO ] ===> Job 96419: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051417_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051417_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051417_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 22:11:38 [INFO ] ===> Job 96420: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051423_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051423_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051423_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 22:11:38 [INFO ] ===> Job 96421: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051428_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051428_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051428_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 22:11:38 [INFO ] ===> Job 96422: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051431_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051431_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051431_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 22:11:38 [INFO ] ===> Job 96423: samtools view -f 4 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051442_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051442_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051442_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051442.fastq 22:11:38 [INFO ] ===> Job 96424: samtools view -f 4 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051444_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051444_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051444_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051444.fastq 22:11:38 [INFO ] ===> Job 96425: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051450_bwa.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051450_bwa.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051450_bwa.bam > ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 22:11:53 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 22:12:04 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 22:12:10 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 22:12:16 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 22:12:36 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 22:12:37 [INFO ] Running step pathogenAlignment... 22:12:37 [INFO ] Building BWA index file for influenzaA... 22:12:37 [INFO ] BWA index for influenzaA already built. 22:12:37 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96426: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051417_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051417_2.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_bwa.sam 22:12:37 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96427: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051423_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051423_2.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_bwa.sam 22:12:37 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96428: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051428_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051428_2.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_bwa.sam 22:12:37 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96429: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051431_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051431_2.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_bwa.sam 22:12:37 [INFO ] Mapping DRR051442.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96430: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051442.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_bwa.sam 22:12:37 [INFO ] Mapping DRR051444.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96431: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051444.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_bwa.sam 22:12:37 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 22:12:37 [INFO ] ===> Job 96432: bwa mem -t 16 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051450_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051450_2.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_bwa.sam 22:12:41 [INFO ] Running step sort... 22:12:41 [INFO ] Sorting run with ID DRR051417 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96433: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_bwa.sam 22:12:42 [INFO ] ===> Job 96434: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam 22:12:42 [INFO ] Sorting run with ID DRR051423 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96435: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_bwa.sam 22:12:42 [INFO ] ===> Job 96436: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam 22:12:42 [INFO ] Sorting run with ID DRR051428 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96437: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_bwa.sam 22:12:42 [INFO ] ===> Job 96438: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam 22:12:42 [INFO ] Sorting run with ID DRR051431 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96439: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_bwa.sam 22:12:42 [INFO ] ===> Job 96440: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam 22:12:42 [INFO ] Sorting run with ID DRR051442 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96441: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_bwa.sam 22:12:42 [INFO ] ===> Job 96442: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam 22:12:42 [INFO ] Sorting run with ID DRR051444 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96443: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_bwa.sam 22:12:42 [INFO ] ===> Job 96444: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.bam 22:12:42 [INFO ] Sorting run with ID DRR051450 vs influenzaA BAM file... 22:12:42 [INFO ] ===> Job 96445: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_bwa.sam 22:12:42 [INFO ] ===> Job 96446: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam 22:12:51 [INFO ] Running step runQualimap... 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051417 vs influenzaA... 22:12:51 [INFO ] ===> Job 96447: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051417 -nt 16 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051423 vs influenzaA... 22:12:51 [INFO ] ===> Job 96448: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051423 -nt 16 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051428 vs influenzaA... 22:12:51 [INFO ] ===> Job 96449: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051428 -nt 16 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051431 vs influenzaA... 22:12:51 [INFO ] ===> Job 96450: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051431 -nt 16 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051442 vs influenzaA... 22:12:51 [INFO ] ===> Job 96451: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051442 -nt 16 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051444 vs influenzaA... 22:12:51 [INFO ] ===> Job 96452: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051444 -nt 16 22:12:51 [INFO ] Analyzing the alignment of run with ID DRR051450 vs influenzaA... 22:12:51 [INFO ] ===> Job 96453: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051450 -nt 16 22:13:03 [INFO ] Running step discardHighError... 22:13:03 [INFO ] Discarding high error runs... 22:13:03 [INFO ] Discarded run DRR051444. 22:13:03 [INFO ] Running step callReditools... 22:13:03 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices/influenzaA/ 22:13:03 [INFO ] Building Samtools index file for influenzaA... 22:13:03 [INFO ] Samtools index for influenzaA already built. 22:13:03 [INFO ] Running SNV calling with Reditools2: DRR051417 vs influenzaA... 22:13:03 [INFO ] ===> Job 96454: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam 22:13:03 [INFO ] Running SNV calling with Reditools2: DRR051423 vs influenzaA... 22:13:03 [INFO ] ===> Job 96455: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam 22:13:03 [INFO ] Running SNV calling with Reditools2: DRR051428 vs influenzaA... 22:13:03 [INFO ] ===> Job 96456: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam 22:13:03 [INFO ] Running SNV calling with Reditools2: DRR051431 vs influenzaA... 22:13:03 [INFO ] ===> Job 96457: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam 22:13:03 [INFO ] Running SNV calling with Reditools2: DRR051442 vs influenzaA... 22:13:03 [INFO ] ===> Job 96458: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam 22:13:03 [INFO ] Running SNV calling with Reditools2: DRR051450 vs influenzaA... 22:13:03 [INFO ] ===> Job 96459: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam 22:13:05 [INFO ] ===> Job 96460: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051417.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051417.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:13:05 [INFO ] ===> Job 96461: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051423.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051423.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:13:05 [INFO ] ===> Job 96462: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051428.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051428.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:13:05 [INFO ] ===> Job 96463: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051431.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051431.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:13:05 [INFO ] ===> Job 96464: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051442.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051442.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:13:05 [INFO ] ===> Job 96465: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051450.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051450.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:13:38 [INFO ] Running step callJacusa... 22:13:38 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices 22:13:38 [INFO ] Running SNV calling with JACUSA: DRR051417 vs influenzaA... 22:13:38 [INFO ] ===> Job 96466: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam 22:13:38 [INFO ] Running SNV calling with JACUSA: DRR051423 vs influenzaA... 22:13:38 [INFO ] ===> Job 96467: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam 22:13:38 [INFO ] Running SNV calling with JACUSA: DRR051428 vs influenzaA... 22:13:38 [INFO ] ===> Job 96468: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam 22:13:38 [INFO ] Running SNV calling with JACUSA: DRR051431 vs influenzaA... 22:13:38 [INFO ] ===> Job 96469: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam 22:13:38 [INFO ] Running SNV calling with JACUSA: DRR051442 vs influenzaA... 22:13:38 [INFO ] ===> Job 96470: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam 22:13:38 [INFO ] Running SNV calling with JACUSA: DRR051450 vs influenzaA... 22:13:38 [INFO ] ===> Job 96471: ../tools/jdk-13.0.2/bin/java -jar ../tools/jacusa/JACUSA_v2.0.2-RC.jar call-1 -p 16 -r ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam 22:13:45 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 22:13:45 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 22:13:45 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 22:13:45 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 22:13:45 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 22:13:46 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 22:13:46 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 22:13:46 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 22:13:46 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 22:13:46 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 22:13:46 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 22:13:46 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 22:13:46 [INFO ] Running step filterSOR... 22:13:46 [INFO ] ===> Job 96472: 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_bwa.bam 22:13:46 [INFO ] ===> Job 96473: 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_bwa.bam 22:13:46 [INFO ] ===> Job 96474: 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_bwa.bam 22:13:46 [INFO ] ===> Job 96475: 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_bwa.bam 22:13:46 [INFO ] ===> Job 96476: 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_bwa.bam 22:13:46 [INFO ] ===> Job 96477: 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_bwa.bam 22:13:58 [INFO ] Analyzing DRR051417... 22:13:59 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051417_filtered.hdf 22:14:00 [INFO ] Analyzing DRR051423... 22:14:00 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051423_filtered.hdf 22:14:01 [INFO ] Analyzing DRR051428... 22:14:01 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051428_filtered.hdf 22:14:01 [INFO ] Analyzing DRR051431... 22:14:02 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051431_filtered.hdf 22:14:02 [INFO ] Analyzing DRR051442... 22:14:02 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051442_filtered.hdf 22:14:03 [INFO ] Analyzing DRR051450... 22:14:03 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051450_filtered.hdf 22:14:04 [INFO ] Running step runSnpEff... 22:14:04 [INFO ] ===> cp ../tools/snpEff/snpEff.config ../influenzaA/ 22:14:04 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA 22:14:07 [INFO ] ===> Job 96478: ../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 22:14:07 [INFO ] ===> Job 96479: ../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 22:14:07 [INFO ] ===> Job 96480: ../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 22:14:07 [INFO ] ===> Job 96481: ../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 22:14:07 [INFO ] ===> Job 96482: ../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 22:14:07 [INFO ] ===> Job 96483: ../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 22:14:07 [INFO ] ===> Job 96484: ../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 22:14:07 [INFO ] ===> Job 96485: ../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 22:14:07 [INFO ] ===> Job 96486: ../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 22:14:07 [INFO ] ===> Job 96487: ../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 22:14:07 [INFO ] ===> Job 96488: ../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 22:14:07 [INFO ] ===> Job 96489: ../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 22:14:18 [INFO ] Running step mergeCalling... 22:14:18 [INFO ] Analyzing calling results from DRR051417 vs influenzaA... 22:14:19 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/reditools.csv 22:14:19 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/jacusa.csv 22:14:20 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/runCommon.csv 22:14:20 [INFO ] Analyzing calling results from DRR051423 vs influenzaA... 22:14:20 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/reditools.csv 22:14:20 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/jacusa.csv 22:14:21 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/runCommon.csv 22:14:21 [INFO ] Analyzing calling results from DRR051428 vs influenzaA... 22:14:21 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/reditools.csv 22:14:22 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/jacusa.csv 22:14:22 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/runCommon.csv 22:14:22 [INFO ] Analyzing calling results from DRR051431 vs influenzaA... 22:14:22 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/reditools.csv 22:14:23 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/jacusa.csv 22:14:23 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/runCommon.csv 22:14:23 [INFO ] Analyzing calling results from DRR051442 vs influenzaA... 22:14:24 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/reditools.csv 22:14:24 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/jacusa.csv 22:14:24 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/runCommon.csv 22:14:25 [INFO ] Analyzing calling results from DRR051450 vs influenzaA... 22:14:25 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/reditools.csv 22:14:25 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/jacusa.csv 22:14:26 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/runCommon.csv 22:14:26 [INFO ] 2028 positions were found. 22:14:26 [INFO ] Generating global files... 22:14:26 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalReditools.csv 22:14:26 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalJacusa.csv 22:14:26 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalCommon.csv 22:14:26 [INFO ] Generating graphs... 22:14:26 [INFO ] Generating graphs for DRR051417 vs influenzaA... 22:14:50 [INFO ] Generating graphs for DRR051423 vs influenzaA... 22:15:12 [INFO ] Generating graphs for DRR051428 vs influenzaA... 22:15:37 [INFO ] Generating graphs for DRR051431 vs influenzaA... 22:16:01 [INFO ] Generating graphs for DRR051442 vs influenzaA... 22:16:25 [INFO ] Generating graphs for DRR051450 vs influenzaA... 22:16:50 [INFO ] Generating global graphs for influenzaA... 22:18:28 [INFO ] Generating analysis report...