02:29:46 [INFO ] Resuming from step hostAlignment... 02:29:49 [INFO ] ===> fastq-dump 02:29:49 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 02:29:49 [INFO ] ===> samtools 02:29:49 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 02:29:50 [INFO ] ===> ../tools/FastQC/fastqc 02:29:50 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 02:29:51 [INFO ] ===> bcftools 02:29:51 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 02:29:51 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 02:29:52 [INFO ] ===> bwa 02:29:52 [INFO ] Running step hostAlignment... 02:29:52 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 02:30:02 [INFO ] Building BWA index file for Homo_sapiens_GRCh38... 02:30:02 [INFO ] ===> cp ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 02:30:13 [INFO ] ===> Job 96247: bwa index -a bwtsw ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38 > ../influenzaA/2-alignment/host/indices/bwa/Homo_sapiens_GRCh38_bwa.done 02:30:13 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96248: bwa mem -t 16 -k 50 -w 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 02:30:13 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96249: bwa mem -t 16 -k 50 -w 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 02:30:13 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96250: bwa mem -t 16 -k 50 -w 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 02:30:13 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96251: bwa mem -t 16 -k 50 -w 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 02:30:13 [INFO ] Mapping DRR051442.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96252: bwa mem -t 16 -k 50 -w 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 02:30:13 [INFO ] Mapping DRR051444.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96253: bwa mem -t 16 -k 50 -w 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 02:30:13 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 02:30:13 [INFO ] ===> Job 96254: bwa mem -t 16 -k 50 -w 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 03:19:53 [INFO ] Running step removeAligned... 03:19:53 [INFO ] ===> Job 96255: 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 03:19:53 [INFO ] ===> Job 96256: 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 03:19:53 [INFO ] ===> Job 96257: 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 03:19:53 [INFO ] ===> Job 96258: 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 03:19:53 [INFO ] ===> Job 96259: 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 03:19:53 [INFO ] ===> Job 96260: 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 03:19:53 [INFO ] ===> Job 96261: 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 03:20:17 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 03:20:31 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 03:20:38 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 03:20:48 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 03:21:15 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 03:21:17 [INFO ] Running step pathogenAlignment... 03:21:17 [INFO ] Building BWA index file for influenzaA... 03:21:17 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA 03:21:17 [INFO ] ===> Job 96262: bwa index ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA > ../influenzaA/2-alignment/pathogen/indices/bwa/influenzaA_bwa.done 03:21:17 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96263: 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 03:21:17 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96264: 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 03:21:17 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96265: 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 03:21:17 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96266: 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 03:21:17 [INFO ] Mapping DRR051442.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96267: 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 03:21:17 [INFO ] Mapping DRR051444.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96268: 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 03:21:17 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 03:21:17 [INFO ] ===> Job 96269: 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 03:21:23 [INFO ] Running step sort... 03:21:23 [INFO ] Sorting run with ID DRR051417 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96270: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_bwa.sam 03:21:24 [INFO ] ===> Job 96271: 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 03:21:24 [INFO ] Sorting run with ID DRR051423 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96272: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_bwa.sam 03:21:24 [INFO ] ===> Job 96273: 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 03:21:24 [INFO ] Sorting run with ID DRR051428 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96274: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_bwa.sam 03:21:24 [INFO ] ===> Job 96275: 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 03:21:24 [INFO ] Sorting run with ID DRR051431 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96276: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_bwa.sam 03:21:24 [INFO ] ===> Job 96277: 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 03:21:24 [INFO ] Sorting run with ID DRR051442 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96278: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_bwa.sam 03:21:24 [INFO ] ===> Job 96279: 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 03:21:24 [INFO ] Sorting run with ID DRR051444 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96280: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_bwa.sam 03:21:24 [INFO ] ===> Job 96281: 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 03:21:24 [INFO ] Sorting run with ID DRR051450 vs influenzaA BAM file... 03:21:24 [INFO ] ===> Job 96282: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_bwa.sam 03:21:24 [INFO ] ===> Job 96283: 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 03:21:35 [INFO ] Running step runQualimap... 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051417 vs influenzaA... 03:21:35 [INFO ] ===> Job 96284: ../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 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051423 vs influenzaA... 03:21:35 [INFO ] ===> Job 96285: ../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 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051428 vs influenzaA... 03:21:35 [INFO ] ===> Job 96286: ../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 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051431 vs influenzaA... 03:21:35 [INFO ] ===> Job 96287: ../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 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051442 vs influenzaA... 03:21:35 [INFO ] ===> Job 96288: ../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 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051444 vs influenzaA... 03:21:35 [INFO ] ===> Job 96289: ../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 03:21:35 [INFO ] Analyzing the alignment of run with ID DRR051450 vs influenzaA... 03:21:35 [INFO ] ===> Job 96290: ../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 03:21:46 [INFO ] Running step discardHighError... 03:21:46 [INFO ] Discarding high error runs... 03:21:46 [INFO ] Discarded run DRR051444. 03:21:46 [INFO ] Running step callReditools... 03:21:46 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices/influenzaA/ 03:21:46 [INFO ] Building Samtools index file for influenzaA... 03:21:46 [INFO ] Samtools index for influenzaA already built. 03:21:46 [INFO ] Running SNV calling with Reditools2: DRR051417 vs influenzaA... 03:21:46 [INFO ] ===> Job 96291: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_bwa.bam 03:21:46 [INFO ] Running SNV calling with Reditools2: DRR051423 vs influenzaA... 03:21:46 [INFO ] ===> Job 96292: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_bwa.bam 03:21:46 [INFO ] Running SNV calling with Reditools2: DRR051428 vs influenzaA... 03:21:46 [INFO ] ===> Job 96293: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_bwa.bam 03:21:46 [INFO ] Running SNV calling with Reditools2: DRR051431 vs influenzaA... 03:21:46 [INFO ] ===> Job 96294: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_bwa.bam 03:21:46 [INFO ] Running SNV calling with Reditools2: DRR051442 vs influenzaA... 03:21:46 [INFO ] ===> Job 96295: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_bwa.bam 03:21:46 [INFO ] Running SNV calling with Reditools2: DRR051450 vs influenzaA... 03:21:46 [INFO ] ===> Job 96296: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_bwa.bam 03:21:49 [INFO ] ===> Job 96297: ../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 03:21:49 [INFO ] ===> Job 96298: ../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 03:21:49 [INFO ] ===> Job 96299: ../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 03:21:49 [INFO ] ===> Job 96300: ../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 03:21:49 [INFO ] ===> Job 96301: ../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 03:21:49 [INFO ] ===> Job 96302: ../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 03:22:35 [INFO ] Running step callJacusa... 03:22:35 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices 03:22:35 [INFO ] Running SNV calling with JACUSA: DRR051417 vs influenzaA... 03:22:35 [INFO ] ===> Job 96303: ../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 03:22:35 [INFO ] Running SNV calling with JACUSA: DRR051423 vs influenzaA... 03:22:35 [INFO ] ===> Job 96304: ../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 03:22:35 [INFO ] Running SNV calling with JACUSA: DRR051428 vs influenzaA... 03:22:35 [INFO ] ===> Job 96305: ../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 03:22:35 [INFO ] Running SNV calling with JACUSA: DRR051431 vs influenzaA... 03:22:35 [INFO ] ===> Job 96306: ../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 03:22:35 [INFO ] Running SNV calling with JACUSA: DRR051442 vs influenzaA... 03:22:35 [INFO ] ===> Job 96307: ../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 03:22:35 [INFO ] Running SNV calling with JACUSA: DRR051450 vs influenzaA... 03:22:35 [INFO ] ===> Job 96308: ../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 03:22:43 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 03:22:43 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 03:22:43 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 03:22:43 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 03:22:43 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 03:22:43 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 03:22:43 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 03:22:43 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 03:22:43 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 03:22:43 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 03:22:43 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 03:22:43 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 03:22:44 [INFO ] Running step filterSOR... 03:22:44 [INFO ] ===> Job 96309: 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 03:22:44 [INFO ] ===> Job 96310: 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 03:22:44 [INFO ] ===> Job 96311: 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 03:22:44 [INFO ] ===> Job 96312: 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 03:22:44 [INFO ] ===> Job 96313: 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 03:22:44 [INFO ] ===> Job 96314: 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 03:23:00 [INFO ] Analyzing DRR051417... 03:23:00 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051417_filtered.hdf 03:23:02 [INFO ] Analyzing DRR051423... 03:23:02 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051423_filtered.hdf 03:23:03 [INFO ] Analyzing DRR051428... 03:23:03 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051428_filtered.hdf 03:23:04 [INFO ] Analyzing DRR051431... 03:23:04 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051431_filtered.hdf 03:23:05 [INFO ] Analyzing DRR051442... 03:23:05 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051442_filtered.hdf 03:23:06 [INFO ] Analyzing DRR051450... 03:23:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051450_filtered.hdf 03:23:06 [INFO ] Running step runSnpEff... 03:23:06 [INFO ] ===> cp ../tools/snpEff/snpEff.config ../influenzaA/ 03:23:07 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA 03:23:10 [INFO ] ===> Job 96315: ../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 03:23:10 [INFO ] ===> Job 96316: ../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 03:23:10 [INFO ] ===> Job 96317: ../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 03:23:10 [INFO ] ===> Job 96318: ../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 03:23:10 [INFO ] ===> Job 96319: ../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 03:23:10 [INFO ] ===> Job 96320: ../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 03:23:10 [INFO ] ===> Job 96321: ../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 03:23:10 [INFO ] ===> Job 96322: ../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 03:23:10 [INFO ] ===> Job 96323: ../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 03:23:10 [INFO ] ===> Job 96324: ../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 03:23:10 [INFO ] ===> Job 96325: ../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 03:23:10 [INFO ] ===> Job 96326: ../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 03:23:23 [INFO ] Running step mergeCalling... 03:23:23 [INFO ] Analyzing calling results from DRR051417 vs influenzaA... 03:23:24 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/reditools.csv 03:23:25 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/jacusa.csv 03:23:25 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/runCommon.csv 03:23:26 [INFO ] Analyzing calling results from DRR051423 vs influenzaA... 03:23:26 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/reditools.csv 03:23:26 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/jacusa.csv 03:23:27 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/runCommon.csv 03:23:27 [INFO ] Analyzing calling results from DRR051428 vs influenzaA... 03:23:27 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/reditools.csv 03:23:28 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/jacusa.csv 03:23:28 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/runCommon.csv 03:23:29 [INFO ] Analyzing calling results from DRR051431 vs influenzaA... 03:23:29 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/reditools.csv 03:23:30 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/jacusa.csv 03:23:30 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/runCommon.csv 03:23:30 [INFO ] Analyzing calling results from DRR051442 vs influenzaA... 03:23:31 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/reditools.csv 03:23:31 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/jacusa.csv 03:23:32 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/runCommon.csv 03:23:32 [INFO ] Analyzing calling results from DRR051450 vs influenzaA... 03:23:32 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/reditools.csv 03:23:33 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/jacusa.csv 03:23:33 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/runCommon.csv 03:23:33 [INFO ] 2204 positions were found. 03:23:33 [INFO ] Generating global files... 03:23:33 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalReditools.csv 03:23:33 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalJacusa.csv 03:23:33 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalCommon.csv 03:23:34 [INFO ] Generating graphs... 03:23:34 [INFO ] Generating graphs for DRR051417 vs influenzaA... 03:24:02 [INFO ] Generating graphs for DRR051423 vs influenzaA... 03:24:25 [INFO ] Generating graphs for DRR051428 vs influenzaA... 03:24:50 [INFO ] Generating graphs for DRR051431 vs influenzaA... 03:25:15 [INFO ] Generating graphs for DRR051442 vs influenzaA... 03:25:40 [INFO ] Generating graphs for DRR051450 vs influenzaA... 03:26:05 [INFO ] Generating global graphs for influenzaA... 03:27:46 [INFO ] Generating analysis report...