21:57:11 [INFO ] Resuming from step hostAlignment... 21:57:15 [INFO ] ===> fastq-dump 21:57:15 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 21:57:15 [INFO ] ===> samtools 21:57:15 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 21:57:16 [INFO ] ===> ../tools/FastQC/fastqc 21:57:16 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 21:57:16 [INFO ] ===> bcftools 21:57:16 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 21:57:17 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 21:57:18 [INFO ] ===> bwa 21:57:18 [INFO ] Running step hostAlignment... 21:57:18 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 21:57:43 [INFO ] Building BWA index file for Homo_sapiens_GRCh38... 21:57:43 [INFO ] BWA index for Homo_sapiens_GRCh38 already built. 21:57:43 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96327: bwa mem -t 16 -k 50 ../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 21:57:43 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96328: bwa mem -t 16 -k 50 ../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 21:57:43 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96329: bwa mem -t 16 -k 50 ../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 21:57:43 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96330: bwa mem -t 16 -k 50 ../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 21:57:43 [INFO ] Mapping DRR051442.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96331: bwa mem -t 16 -k 50 ../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 21:57:43 [INFO ] Mapping DRR051444.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96332: bwa mem -t 16 -k 50 ../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 21:57:43 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 21:57:43 [INFO ] ===> Job 96333: bwa mem -t 16 -k 50 ../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 21:58:46 [INFO ] Running step removeAligned... 21:58:46 [INFO ] ===> Job 96334: 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 21:58:46 [INFO ] ===> Job 96335: 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 21:58:46 [INFO ] ===> Job 96336: 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 21:58:46 [INFO ] ===> Job 96337: 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 21:58:46 [INFO ] ===> Job 96338: 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 21:58:46 [INFO ] ===> Job 96339: 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 21:58:46 [INFO ] ===> Job 96340: 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 21:59:10 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 21:59:23 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 21:59:31 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 21:59:40 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 22:00:07 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 22:00:10 [INFO ] Running step pathogenAlignment... 22:00:10 [INFO ] Building BWA index file for influenzaA... 22:00:10 [INFO ] BWA index for influenzaA already built. 22:00:10 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96341: bwa mem -t 16 -k 50 ../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 22:00:10 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96342: bwa mem -t 16 -k 50 ../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 22:00:10 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96343: bwa mem -t 16 -k 50 ../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 22:00:10 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96344: bwa mem -t 16 -k 50 ../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 22:00:10 [INFO ] Mapping DRR051442.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96345: bwa mem -t 16 -k 50 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051442.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_bwa.sam 22:00:10 [INFO ] Mapping DRR051444.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96346: bwa mem -t 16 -k 50 ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA ../influenzaA/2-alignment/host/fastq/DRR051444.fastq > ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_bwa.sam 22:00:10 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 22:00:10 [INFO ] ===> Job 96347: bwa mem -t 16 -k 50 ../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 22:00:16 [INFO ] Running step sort... 22:00:16 [INFO ] Sorting run with ID DRR051417 vs influenzaA BAM file... 22:00:16 [INFO ] ===> Job 96348: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_bwa.sam 22:00:16 [INFO ] ===> Job 96349: 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 22:00:16 [INFO ] Sorting run with ID DRR051423 vs influenzaA BAM file... 22:00:16 [INFO ] ===> Job 96350: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_bwa.sam 22:00:16 [INFO ] ===> Job 96351: 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 22:00:16 [INFO ] Sorting run with ID DRR051428 vs influenzaA BAM file... 22:00:16 [INFO ] ===> Job 96352: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_bwa.sam 22:00:17 [INFO ] ===> Job 96353: 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 22:00:17 [INFO ] Sorting run with ID DRR051431 vs influenzaA BAM file... 22:00:17 [INFO ] ===> Job 96354: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_bwa.sam 22:00:17 [INFO ] ===> Job 96355: 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 22:00:17 [INFO ] Sorting run with ID DRR051442 vs influenzaA BAM file... 22:00:17 [INFO ] ===> Job 96356: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_bwa.sam 22:00:17 [INFO ] ===> Job 96357: 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 22:00:17 [INFO ] Sorting run with ID DRR051444 vs influenzaA BAM file... 22:00:17 [INFO ] ===> Job 96358: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_bwa.sam 22:00:17 [INFO ] ===> Job 96359: 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 22:00:17 [INFO ] Sorting run with ID DRR051450 vs influenzaA BAM file... 22:00:17 [INFO ] ===> Job 96360: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_bwa.sam 22:00:17 [INFO ] ===> Job 96361: 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 22:00:27 [INFO ] Running step runQualimap... 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051417 vs influenzaA... 22:00:27 [INFO ] ===> Job 96362: ../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 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051423 vs influenzaA... 22:00:27 [INFO ] ===> Job 96363: ../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 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051428 vs influenzaA... 22:00:27 [INFO ] ===> Job 96364: ../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 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051431 vs influenzaA... 22:00:27 [INFO ] ===> Job 96365: ../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 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051442 vs influenzaA... 22:00:27 [INFO ] ===> Job 96366: ../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 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051444 vs influenzaA... 22:00:27 [INFO ] ===> Job 96367: ../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 22:00:27 [INFO ] Analyzing the alignment of run with ID DRR051450 vs influenzaA... 22:00:27 [INFO ] ===> Job 96368: ../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 22:00:38 [INFO ] Running step discardHighError... 22:00:38 [INFO ] Discarding high error runs... 22:00:38 [INFO ] No runs were discarded. 22:00:38 [INFO ] Running step callReditools... 22:00:38 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices/influenzaA/ 22:00:38 [INFO ] Building Samtools index file for influenzaA... 22:00:38 [INFO ] ===> Job 96369: samtools faidx ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa > ../influenzaA/4-snvCalling/indices/influenzaA/influenzaA_faidx.done 22:00:38 [INFO ] Running SNV calling with Reditools2: DRR051417 vs influenzaA... 22:00:38 [INFO ] ===> Job 96370: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam 22:00:38 [INFO ] Running SNV calling with Reditools2: DRR051423 vs influenzaA... 22:00:38 [INFO ] ===> Job 96371: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam 22:00:38 [INFO ] Running SNV calling with Reditools2: DRR051428 vs influenzaA... 22:00:38 [INFO ] ===> Job 96372: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam 22:00:38 [INFO ] Running SNV calling with Reditools2: DRR051431 vs influenzaA... 22:00:38 [INFO ] ===> Job 96373: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam 22:00:38 [INFO ] Running SNV calling with Reditools2: DRR051442 vs influenzaA... 22:00:39 [INFO ] ===> Job 96374: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam 22:00:39 [INFO ] Running SNV calling with Reditools2: DRR051444 vs influenzaA... 22:00:39 [INFO ] ===> Job 96375: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.bam 22:00:39 [INFO ] Running SNV calling with Reditools2: DRR051450 vs influenzaA... 22:00:39 [INFO ] ===> Job 96376: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam 22:00:41 [INFO ] ===> Job 96377: ../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 22:00:41 [INFO ] ===> Job 96378: ../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 22:00:41 [INFO ] ===> Job 96379: ../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 22:00:41 [INFO ] ===> Job 96380: ../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 22:00:41 [INFO ] ===> Job 96381: ../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 22:00:41 [INFO ] ===> Job 96382: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.bam -r ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa -m ../influenzaA/4-snvCalling/homopol/influenzaA/DRR051444.homopol.txt -o ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051444.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 22:00:42 [INFO ] ===> Job 96383: ../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 22:01:18 [INFO ] Running step callJacusa... 22:01:18 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051417 vs influenzaA... 22:01:18 [INFO ] ===> Job 96384: ../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 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051423 vs influenzaA... 22:01:18 [INFO ] ===> Job 96385: ../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 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051428 vs influenzaA... 22:01:18 [INFO ] ===> Job 96386: ../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 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051431 vs influenzaA... 22:01:18 [INFO ] ===> Job 96387: ../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 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051442 vs influenzaA... 22:01:18 [INFO ] ===> Job 96388: ../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 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051444 vs influenzaA... 22:01:18 [INFO ] ===> Job 96389: ../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/DRR051444.jacusa.vcf -s -f V -m 25 -q 35 -a B,I,Y ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.bam 22:01:18 [INFO ] Running SNV calling with JACUSA: DRR051450 vs influenzaA... 22:01:18 [INFO ] ===> Job 96390: ../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 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 22:01:26 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 22:01:26 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 22:01:26 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 22:01:26 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 22:01:26 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.vcf.pre 22:01:26 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.vcf.pre 22:01:26 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 22:01:27 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 22:01:27 [INFO ] Running step filterSOR... 22:01:27 [INFO ] ===> Job 96391: 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 22:01:27 [INFO ] ===> Job 96392: 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 22:01:27 [INFO ] ===> Job 96393: 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 22:01:27 [INFO ] ===> Job 96394: 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 22:01:27 [INFO ] ===> Job 96395: 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 22:01:27 [INFO ] ===> Job 96396: 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/DRR051444.mpileup.vcf ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.bam 22:01:27 [INFO ] ===> Job 96397: 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 22:01:40 [INFO ] Analyzing DRR051417... 22:01:42 [INFO ] Analyzing DRR051423... 22:01:43 [INFO ] Analyzing DRR051428... 22:01:43 [INFO ] Analyzing DRR051431... 22:01:44 [INFO ] Analyzing DRR051442... 22:01:45 [INFO ] Analyzing DRR051444... 22:01:45 [INFO ] Analyzing DRR051450... 22:01:46 [INFO ] Running step runSnpEff... 22:01:46 [INFO ] ===> cp ../tools/snpEff/snpEff.config ../influenzaA/ 22:01:46 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA 22:01:49 [INFO ] ===> Job 96398: ../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 22:01:49 [INFO ] ===> Job 96399: ../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 22:01:49 [INFO ] ===> Job 96400: ../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 22:01:49 [INFO ] ===> Job 96401: ../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 22:01:49 [INFO ] ===> Job 96402: ../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 22:01:49 [INFO ] ===> Job 96403: ../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 22:01:49 [INFO ] ===> Job 96404: ../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 22:01:50 [INFO ] ===> Job 96405: ../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 22:01:50 [INFO ] ===> Job 96406: ../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 22:01:50 [INFO ] ===> Job 96407: ../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 22:01:50 [INFO ] ===> Job 96408: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/reditools/influenzaA/DRR051444.reditools.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051444.snpeff.reditools.vcf 22:01:50 [INFO ] ===> Job 96409: ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -c ../influenzaA/snpEff.config influenzaA ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.presnpeff.vcf > ../influenzaA/5-snpeff/influenzaA/DRR051444.snpeff.jacusa.vcf 22:01:50 [INFO ] ===> Job 96410: ../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 22:01:50 [INFO ] ===> Job 96411: ../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 22:02:00 [INFO ] Running step mergeCalling... 22:02:00 [INFO ] Analyzing calling results from DRR051417 vs influenzaA... 22:02:02 [INFO ] Analyzing calling results from DRR051423 vs influenzaA... 22:02:03 [INFO ] Analyzing calling results from DRR051428 vs influenzaA... 22:02:04 [INFO ] Analyzing calling results from DRR051431 vs influenzaA... 22:02:06 [INFO ] Analyzing calling results from DRR051442 vs influenzaA... 22:02:07 [INFO ] Analyzing calling results from DRR051444 vs influenzaA... 22:02:08 [INFO ] Analyzing calling results from DRR051450 vs influenzaA... 22:02:09 [INFO ] 1800 positions were found. 22:02:09 [INFO ] Generating global files... 22:02:09 [INFO ] Generating graphs... 22:02:09 [INFO ] Generating graphs for DRR051417 vs influenzaA... 22:02:31 [INFO ] Generating graphs for DRR051423 vs influenzaA... 22:02:50 [INFO ] Generating graphs for DRR051428 vs influenzaA... 22:03:12 [INFO ] Generating graphs for DRR051431 vs influenzaA... 22:03:35 [INFO ] Generating graphs for DRR051442 vs influenzaA... 22:03:53 [INFO ] Generating graphs for DRR051444 vs influenzaA... 22:04:15 [INFO ] Generating graphs for DRR051450 vs influenzaA... 22:04:37 [INFO ] Generating global graphs for influenzaA... 22:06:15 [INFO ] Generating analysis report...