01:06:49 [INFO ] Resuming from step hostAlignment... 01:07:02 [INFO ] ===> fastq-dump 01:07:02 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 01:07:04 [INFO ] ===> samtools 01:07:04 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 01:07:07 [INFO ] ===> ../tools/FastQC/fastqc 01:07:09 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 01:07:10 [INFO ] ===> bcftools 01:07:11 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 01:07:11 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 01:07:14 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 01:07:15 [INFO ] Running step hostAlignment... 01:07:15 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 01:07:31 [INFO ] Building Hisat2 index for Homo_sapiens_GRCh38... 01:07:32 [INFO ] ===> Job 96161: ../tools/hisat2-2.1.0/hisat2-build -p 16 ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 > ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38_hisat2.done 01:07:32 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96162: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -1 ../influenzaA/1-quality/fastq/DRR051417_1.fastq -2 ../influenzaA/1-quality/fastq/DRR051417_2.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051417_hisat2.sam -p 16 01:07:32 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96163: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -1 ../influenzaA/1-quality/fastq/DRR051423_1.fastq -2 ../influenzaA/1-quality/fastq/DRR051423_2.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051423_hisat2.sam -p 16 01:07:32 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96164: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -1 ../influenzaA/1-quality/fastq/DRR051428_1.fastq -2 ../influenzaA/1-quality/fastq/DRR051428_2.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051428_hisat2.sam -p 16 01:07:32 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96165: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -1 ../influenzaA/1-quality/fastq/DRR051431_1.fastq -2 ../influenzaA/1-quality/fastq/DRR051431_2.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051431_hisat2.sam -p 16 01:07:32 [INFO ] Mapping DRR051442.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96166: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -U ../influenzaA/1-quality/fastq/DRR051442.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051442_hisat2.sam -p 16 01:07:32 [INFO ] Mapping DRR051444.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96167: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -U ../influenzaA/1-quality/fastq/DRR051444.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051444_hisat2.sam -p 16 01:07:32 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 01:07:32 [INFO ] ===> Job 96168: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/host/indices/hisat2/Homo_sapiens_GRCh38 -1 ../influenzaA/1-quality/fastq/DRR051450_1.fastq -2 ../influenzaA/1-quality/fastq/DRR051450_2.fastq -S ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051450_hisat2.sam -p 16 01:27:21 [INFO ] Running step removeAligned... 01:27:21 [INFO ] ===> Job 96169: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051417_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051417_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051417_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 01:27:21 [INFO ] ===> Job 96170: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051423_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051423_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051423_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 01:27:21 [INFO ] ===> Job 96171: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051428_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051428_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051428_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 01:27:21 [INFO ] ===> Job 96172: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051431_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051431_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051431_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 01:27:21 [INFO ] ===> Job 96173: samtools view -f 4 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051442_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051442_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051442_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051442.fastq 01:27:21 [INFO ] ===> Job 96174: samtools view -f 4 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051444_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051444_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051444_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051444.fastq 01:27:21 [INFO ] ===> Job 96175: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051450_hisat2.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051450_hisat2.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051450_hisat2.bam > ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 01:27:54 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 01:28:07 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 01:28:17 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 01:28:27 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 01:28:56 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 01:28:57 [INFO ] Running step pathogenAlignment... 01:28:57 [INFO ] Building Hisat2 index for influenzaA... 01:28:57 [INFO ] ===> Job 96176: ../tools/hisat2-2.1.0/hisat2-build -p 16 ../influenzaA/data/influenzaA/genome.fa ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA > ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA_hisat2.done 01:28:57 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 01:28:57 [INFO ] ===> Job 96177: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -1 ../influenzaA/2-alignment/host/fastq/DRR051417_1.fastq -2 ../influenzaA/2-alignment/host/fastq/DRR051417_2.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_hisat2.sam -p 16 01:28:57 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 01:28:57 [INFO ] ===> Job 96178: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -1 ../influenzaA/2-alignment/host/fastq/DRR051423_1.fastq -2 ../influenzaA/2-alignment/host/fastq/DRR051423_2.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_hisat2.sam -p 16 01:28:57 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 01:28:57 [INFO ] ===> Job 96179: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -1 ../influenzaA/2-alignment/host/fastq/DRR051428_1.fastq -2 ../influenzaA/2-alignment/host/fastq/DRR051428_2.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_hisat2.sam -p 16 01:28:58 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 01:28:58 [INFO ] ===> Job 96180: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -1 ../influenzaA/2-alignment/host/fastq/DRR051431_1.fastq -2 ../influenzaA/2-alignment/host/fastq/DRR051431_2.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_hisat2.sam -p 16 01:28:58 [INFO ] Mapping DRR051442.fastq to the reference file... 01:28:58 [INFO ] ===> Job 96181: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -U ../influenzaA/2-alignment/host/fastq/DRR051442.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_hisat2.sam -p 16 01:28:58 [INFO ] Mapping DRR051444.fastq to the reference file... 01:28:58 [INFO ] ===> Job 96182: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -U ../influenzaA/2-alignment/host/fastq/DRR051444.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_hisat2.sam -p 16 01:28:58 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 01:28:58 [INFO ] ===> Job 96183: ../tools/hisat2-2.1.0/hisat2 -x ../influenzaA/2-alignment/pathogen/indices/hisat2/influenzaA -1 ../influenzaA/2-alignment/host/fastq/DRR051450_1.fastq -2 ../influenzaA/2-alignment/host/fastq/DRR051450_2.fastq -S ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_hisat2.sam -p 16 01:29:04 [INFO ] Running step sort... 01:29:04 [INFO ] Sorting run with ID DRR051417 vs influenzaA BAM file... 01:29:04 [INFO ] ===> Job 96184: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_hisat2.sam 01:29:04 [INFO ] ===> Job 96185: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_hisat2.bam 01:29:04 [INFO ] Sorting run with ID DRR051423 vs influenzaA BAM file... 01:29:04 [INFO ] ===> Job 96186: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_hisat2.sam 01:29:04 [INFO ] ===> Job 96187: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_hisat2.bam 01:29:04 [INFO ] Sorting run with ID DRR051428 vs influenzaA BAM file... 01:29:04 [INFO ] ===> Job 96188: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_hisat2.sam 01:29:04 [INFO ] ===> Job 96189: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_hisat2.bam 01:29:04 [INFO ] Sorting run with ID DRR051431 vs influenzaA BAM file... 01:29:04 [INFO ] ===> Job 96190: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_hisat2.sam 01:29:04 [INFO ] ===> Job 96191: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_hisat2.bam 01:29:04 [INFO ] Sorting run with ID DRR051442 vs influenzaA BAM file... 01:29:05 [INFO ] ===> Job 96192: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_hisat2.sam 01:29:05 [INFO ] ===> Job 96193: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_hisat2.bam 01:29:05 [INFO ] Sorting run with ID DRR051444 vs influenzaA BAM file... 01:29:05 [INFO ] ===> Job 96194: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_hisat2.sam 01:29:05 [INFO ] ===> Job 96195: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_hisat2.bam 01:29:05 [INFO ] Sorting run with ID DRR051450 vs influenzaA BAM file... 01:29:05 [INFO ] ===> Job 96196: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_hisat2.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_hisat2.sam 01:29:05 [INFO ] ===> Job 96197: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_hisat2.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_hisat2.bam 01:29:14 [INFO ] Running step runQualimap... 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051417 vs influenzaA... 01:29:14 [INFO ] ===> Job 96198: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051417 -nt 16 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051423 vs influenzaA... 01:29:14 [INFO ] ===> Job 96199: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051423 -nt 16 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051428 vs influenzaA... 01:29:14 [INFO ] ===> Job 96200: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051428 -nt 16 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051431 vs influenzaA... 01:29:14 [INFO ] ===> Job 96201: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051431 -nt 16 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051442 vs influenzaA... 01:29:14 [INFO ] ===> Job 96202: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051442 -nt 16 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051444 vs influenzaA... 01:29:14 [INFO ] ===> Job 96203: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051444 -nt 16 01:29:14 [INFO ] Analyzing the alignment of run with ID DRR051450 vs influenzaA... 01:29:14 [INFO ] ===> Job 96204: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_hisat2.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051450 -nt 16 01:29:25 [INFO ] Running step discardHighError... 01:29:25 [INFO ] Discarding high error runs... 01:29:25 [INFO ] No runs were discarded. 01:29:25 [INFO ] Running step callReditools... 01:29:25 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices/influenzaA/ 01:29:26 [INFO ] Building Samtools index file for influenzaA... 01:29:26 [INFO ] Samtools index for influenzaA already built. 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051417 vs influenzaA... 01:29:26 [INFO ] ===> Job 96205: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_hisat2.bam 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051423 vs influenzaA... 01:29:26 [INFO ] ===> Job 96206: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_hisat2.bam 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051428 vs influenzaA... 01:29:26 [INFO ] ===> Job 96207: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_hisat2.bam 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051431 vs influenzaA... 01:29:26 [INFO ] ===> Job 96208: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_hisat2.bam 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051442 vs influenzaA... 01:29:26 [INFO ] ===> Job 96209: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_hisat2.bam 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051444 vs influenzaA... 01:29:26 [INFO ] ===> Job 96210: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_hisat2.bam 01:29:26 [INFO ] Running SNV calling with Reditools2: DRR051450 vs influenzaA... 01:29:26 [INFO ] ===> Job 96211: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_hisat2.bam 01:29:28 [INFO ] ===> Job 96212: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_hisat2.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 01:29:28 [INFO ] ===> Job 96213: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_hisat2.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 01:29:28 [INFO ] ===> Job 96214: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_hisat2.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 01:29:29 [INFO ] ===> Job 96215: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_hisat2.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 01:29:29 [INFO ] ===> Job 96216: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_hisat2.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 01:29:29 [INFO ] ===> Job 96217: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_hisat2.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 01:29:29 [INFO ] ===> Job 96218: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_hisat2.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 01:30:04 [INFO ] Running step callJacusa... 01:30:04 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051417 vs influenzaA... 01:30:04 [INFO ] ===> Job 96219: ../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_hisat2.bam 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051423 vs influenzaA... 01:30:04 [INFO ] ===> Job 96220: ../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_hisat2.bam 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051428 vs influenzaA... 01:30:04 [INFO ] ===> Job 96221: ../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_hisat2.bam 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051431 vs influenzaA... 01:30:04 [INFO ] ===> Job 96222: ../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_hisat2.bam 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051442 vs influenzaA... 01:30:04 [INFO ] ===> Job 96223: ../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_hisat2.bam 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051444 vs influenzaA... 01:30:04 [INFO ] ===> Job 96224: ../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_hisat2.bam 01:30:04 [INFO ] Running SNV calling with JACUSA: DRR051450 vs influenzaA... 01:30:04 [INFO ] ===> Job 96225: ../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_hisat2.bam 01:30:12 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 01:30:12 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 01:30:12 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 01:30:12 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 01:30:12 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 01:30:12 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 01:30:12 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 01:30:12 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 01:30:12 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 01:30:12 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 01:30:12 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.vcf.pre 01:30:12 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051444.jacusa.vcf.pre 01:30:13 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 01:30:13 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 01:30:13 [INFO ] Running step filterSOR... 01:30:13 [INFO ] ===> Job 96226: 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_hisat2.bam 01:30:13 [INFO ] ===> Job 96227: 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_hisat2.bam 01:30:13 [INFO ] ===> Job 96228: 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_hisat2.bam 01:30:13 [INFO ] ===> Job 96229: 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_hisat2.bam 01:30:13 [INFO ] ===> Job 96230: 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_hisat2.bam 01:30:13 [INFO ] ===> Job 96231: 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_hisat2.bam 01:30:13 [INFO ] ===> Job 96232: 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_hisat2.bam 01:30:27 [INFO ] Analyzing DRR051417... 01:30:28 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051417_filtered.hdf 01:30:30 [INFO ] Analyzing DRR051423... 01:30:30 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051423_filtered.hdf 01:30:31 [INFO ] Analyzing DRR051428... 01:30:31 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051428_filtered.hdf 01:30:31 [INFO ] Analyzing DRR051431... 01:30:32 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051431_filtered.hdf 01:30:32 [INFO ] Analyzing DRR051442... 01:30:32 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051442_filtered.hdf 01:30:33 [INFO ] Analyzing DRR051444... 01:30:34 [INFO ] Analyzing DRR051450... 01:30:34 [INFO ] ===> rm ../influenzaA/4-snvCalling/depths/influenzaA/DRR051450_filtered.hdf 01:30:35 [INFO ] Running step runSnpEff... 01:30:35 [INFO ] ===> cp ../tools/snpEff/snpEff.config ../influenzaA/ 01:30:35 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar build -genbank -c ../influenzaA/snpEff.config -v influenzaA 01:30:38 [INFO ] ===> Job 96233: ../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 01:30:38 [INFO ] ===> Job 96234: ../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 01:30:38 [INFO ] ===> Job 96235: ../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 01:30:38 [INFO ] ===> Job 96236: ../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 01:30:38 [INFO ] ===> Job 96237: ../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 01:30:38 [INFO ] ===> Job 96238: ../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 01:30:38 [INFO ] ===> Job 96239: ../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 01:30:38 [INFO ] ===> Job 96240: ../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 01:30:38 [INFO ] ===> Job 96241: ../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 01:30:38 [INFO ] ===> Job 96242: ../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 01:30:38 [INFO ] ===> Job 96243: ../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 01:30:38 [INFO ] ===> Job 96244: ../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 01:30:38 [INFO ] ===> Job 96245: ../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 01:30:39 [INFO ] ===> Job 96246: ../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 01:30:49 [INFO ] Running step mergeCalling... 01:30:49 [INFO ] Analyzing calling results from DRR051417 vs influenzaA... 01:30:50 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/reditools.csv 01:30:51 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/jacusa.csv 01:30:51 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051417/csv/runCommon.csv 01:30:52 [INFO ] Analyzing calling results from DRR051423 vs influenzaA... 01:30:52 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/reditools.csv 01:30:53 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/jacusa.csv 01:30:53 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051423/csv/runCommon.csv 01:30:53 [INFO ] Analyzing calling results from DRR051428 vs influenzaA... 01:30:53 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/reditools.csv 01:30:54 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/jacusa.csv 01:30:54 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051428/csv/runCommon.csv 01:30:55 [INFO ] Analyzing calling results from DRR051431 vs influenzaA... 01:30:55 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/reditools.csv 01:30:55 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/jacusa.csv 01:30:55 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051431/csv/runCommon.csv 01:30:56 [INFO ] Analyzing calling results from DRR051442 vs influenzaA... 01:30:56 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/reditools.csv 01:30:56 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/jacusa.csv 01:30:57 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051442/csv/runCommon.csv 01:30:57 [INFO ] Analyzing calling results from DRR051444 vs influenzaA... 01:30:58 [INFO ] Analyzing calling results from DRR051450 vs influenzaA... 01:30:59 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/reditools.csv 01:30:59 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/jacusa.csv 01:30:59 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/DRR051450/csv/runCommon.csv 01:31:00 [INFO ] 1802 positions were found. 01:31:00 [INFO ] Generating global files... 01:31:00 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalReditools.csv 01:31:00 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalJacusa.csv 01:31:00 [INFO ] ===> rm ../influenzaA/6-visualization/influenzaA/csv/globalCommon.csv 01:31:00 [INFO ] Generating graphs... 01:31:00 [INFO ] Generating graphs for DRR051417 vs influenzaA... 01:31:25 [INFO ] Generating graphs for DRR051423 vs influenzaA... 01:31:38 [INFO ] Generating graphs for DRR051428 vs influenzaA... 01:31:58 [INFO ] Generating graphs for DRR051431 vs influenzaA... 01:32:17 [INFO ] Generating graphs for DRR051442 vs influenzaA... 01:32:36 [INFO ] Generating graphs for DRR051444 vs influenzaA... 01:32:58 [INFO ] Generating graphs for DRR051450 vs influenzaA... 01:33:14 [INFO ] Generating global graphs for influenzaA... 01:33:32 [INFO ] Generating analysis report...