12:59:37 [INFO ] Resuming from step hostAlignment... 12:59:42 [INFO ] ===> fastq-dump 12:59:42 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 12:59:42 [INFO ] ===> samtools 12:59:42 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 12:59:42 [INFO ] ===> ../tools/FastQC/fastqc 12:59:43 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 12:59:43 [INFO ] ===> bcftools 12:59:44 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 12:59:44 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 12:59:45 [INFO ] ===> STAR 12:59:45 [INFO ] Running step hostAlignment... 12:59:45 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 13:00:28 [INFO ] Building STAR index file for Homo_sapiens_GRCh38... 13:00:28 [INFO ] STAR index for Homo_sapiens_GRCh38 already built. 13:00:28 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96011: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051417_1.fastq ../influenzaA/1-quality/fastq/DRR051417_2.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051417 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051417Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051417_star.sam 13:00:28 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96012: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051423_1.fastq ../influenzaA/1-quality/fastq/DRR051423_2.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051423 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051423Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051423_star.sam 13:00:28 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96013: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051428_1.fastq ../influenzaA/1-quality/fastq/DRR051428_2.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051428 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051428Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051428_star.sam 13:00:28 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96014: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051431_1.fastq ../influenzaA/1-quality/fastq/DRR051431_2.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051431 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051431Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051431_star.sam 13:00:28 [INFO ] Mapping DRR051442.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96015: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051442.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051442 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051442Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051442_star.sam 13:00:28 [INFO ] Mapping DRR051444.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96016: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051444.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051444 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051444Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051444_star.sam 13:00:28 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 13:00:28 [INFO ] ===> Job 96017: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/1-quality/fastq/DRR051450_1.fastq ../influenzaA/1-quality/fastq/DRR051450_2.fastq --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051450 --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051450Aligned.out.sam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051450_star.sam 13:04:41 [INFO ] Running step removeAligned... 13:04:41 [INFO ] ===> Job 96018: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051417_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051417_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051417_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 13:04:41 [INFO ] ===> Job 96019: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051423_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051423_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051423_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 13:04:41 [INFO ] ===> Job 96020: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051428_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051428_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051428_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 13:04:41 [INFO ] ===> Job 96021: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051431_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051431_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051431_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 13:04:41 [INFO ] ===> Job 96022: samtools view -f 4 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051442_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051442_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051442_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051442.fastq 13:04:41 [INFO ] ===> Job 96023: samtools view -f 4 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051444_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051444_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051444_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051444.fastq 13:04:41 [INFO ] ===> Job 96024: samtools view -f 13 -F 256 -bo ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051450_star.bam ../influenzaA/2-alignment/host/sam/Homo_sapiens_GRCh38/DRR051450_star.sam && samtools bam2fq ../influenzaA/2-alignment/host/bam/Homo_sapiens_GRCh38/DRR051450_star.bam > ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051417Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051417_1.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051417Unmapped.out.mate2 ../influenzaA/2-alignment/host/fastq/DRR051417_2.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051423Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051423_1.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051423Unmapped.out.mate2 ../influenzaA/2-alignment/host/fastq/DRR051423_2.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051428Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051428_1.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051428Unmapped.out.mate2 ../influenzaA/2-alignment/host/fastq/DRR051428_2.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051431Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051431_1.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051431Unmapped.out.mate2 ../influenzaA/2-alignment/host/fastq/DRR051431_2.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051442Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051442.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051444Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051444.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051450Unmapped.out.mate1 ../influenzaA/2-alignment/host/fastq/DRR051450_1.fastq 13:04:59 [INFO ] ===> mv ../influenzaA/2-alignment/host/star/Homo_sapiens_GRCh38/DRR051450Unmapped.out.mate2 ../influenzaA/2-alignment/host/fastq/DRR051450_2.fastq 13:04:59 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051417.unmapped.fastq 13:04:59 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051423.unmapped.fastq 13:04:59 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051428.unmapped.fastq 13:04:59 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051431.unmapped.fastq 13:04:59 [INFO ] ===> rm ../influenzaA/2-alignment/host/fastq/DRR051450.unmapped.fastq 13:04:59 [INFO ] Running step pathogenAlignment... 13:04:59 [INFO ] Building STAR index file for influenzaA... 13:04:59 [INFO ] ===> Job 96025: STAR --runThreadN 16 --runMode genomeGenerate --genomeSAindexNbases 3 --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --genomeFastaFiles ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/indices/influenzaA_star.done 13:04:59 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96026: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051417_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051417_2.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051417 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051417Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_star.sam 13:04:59 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96027: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051423_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051423_2.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051423 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051423Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_star.sam 13:04:59 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96028: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051428_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051428_2.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051428 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051428Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_star.sam 13:04:59 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96029: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051431_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051431_2.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051431 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051431Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_star.sam 13:04:59 [INFO ] Mapping DRR051442.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96030: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051442.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051442 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051442Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_star.sam 13:04:59 [INFO ] Mapping DRR051444.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96031: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051444.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051444 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051444Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_star.sam 13:04:59 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 13:04:59 [INFO ] ===> Job 96032: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../influenzaA/2-alignment/host/fastq/DRR051450_1.fastq ../influenzaA/2-alignment/host/fastq/DRR051450_2.fastq --genomeDir ../influenzaA/2-alignment/pathogen/indices/influenzaA_star --outFileNamePrefix ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051450 && mv ../influenzaA/2-alignment/pathogen/star/influenzaA/DRR051450Aligned.out.sam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_star.sam 13:06:55 [INFO ] Running step sort... 13:06:55 [INFO ] Sorting run with ID DRR051417 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96033: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051417_star.sam 13:06:55 [INFO ] ===> Job 96034: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.bam 13:06:55 [INFO ] Sorting run with ID DRR051423 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96035: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051423_star.sam 13:06:55 [INFO ] ===> Job 96036: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.bam 13:06:55 [INFO ] Sorting run with ID DRR051428 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96037: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051428_star.sam 13:06:55 [INFO ] ===> Job 96038: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.bam 13:06:55 [INFO ] Sorting run with ID DRR051431 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96039: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051431_star.sam 13:06:55 [INFO ] ===> Job 96040: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.bam 13:06:55 [INFO ] Sorting run with ID DRR051442 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96041: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051442_star.sam 13:06:55 [INFO ] ===> Job 96042: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.bam 13:06:55 [INFO ] Sorting run with ID DRR051444 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96043: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051444_star.sam 13:06:55 [INFO ] ===> Job 96044: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_star.bam 13:06:55 [INFO ] Sorting run with ID DRR051450 vs influenzaA BAM file... 13:06:55 [INFO ] ===> Job 96045: samtools sort -O BAM -o ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.sorted.bam ../influenzaA/2-alignment/pathogen/sam/influenzaA/DRR051450_star.sam 13:06:55 [INFO ] ===> Job 96046: samtools calmd -b ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.sorted.bam ../influenzaA/data/influenzaA/genome.fa > ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.bam 13:06:59 [INFO ] Running step runQualimap... 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051417 vs influenzaA... 13:06:59 [INFO ] ===> Job 96047: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051417 -nt 16 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051423 vs influenzaA... 13:06:59 [INFO ] ===> Job 96048: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051423 -nt 16 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051428 vs influenzaA... 13:06:59 [INFO ] ===> Job 96049: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051428 -nt 16 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051431 vs influenzaA... 13:06:59 [INFO ] ===> Job 96050: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051431 -nt 16 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051442 vs influenzaA... 13:06:59 [INFO ] ===> Job 96051: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051442 -nt 16 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051444 vs influenzaA... 13:06:59 [INFO ] ===> Job 96052: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051444_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051444 -nt 16 13:06:59 [INFO ] Analyzing the alignment of run with ID DRR051450 vs influenzaA... 13:06:59 [INFO ] ===> Job 96053: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.bam -outdir ../influenzaA/3-qualimap/influenzaA/DRR051450 -nt 16 13:07:12 [INFO ] Running step discardHighError... 13:07:12 [INFO ] Discarding high error runs... 13:07:12 [INFO ] Discarded run DRR051444. 13:07:12 [INFO ] Running step callReditools... 13:07:12 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices/influenzaA/ 13:07:12 [INFO ] Building Samtools index file for influenzaA... 13:07:12 [INFO ] ===> Job 96054: samtools faidx ../influenzaA/4-snvCalling/indices/influenzaA/genome.fa > ../influenzaA/4-snvCalling/indices/influenzaA/influenzaA_faidx.done 13:07:12 [INFO ] Running SNV calling with Reditools2: DRR051417 vs influenzaA... 13:07:12 [INFO ] ===> Job 96055: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.bam 13:07:12 [INFO ] Running SNV calling with Reditools2: DRR051423 vs influenzaA... 13:07:12 [INFO ] ===> Job 96056: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.bam 13:07:12 [INFO ] Running SNV calling with Reditools2: DRR051428 vs influenzaA... 13:07:12 [INFO ] ===> Job 96057: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.bam 13:07:12 [INFO ] Running SNV calling with Reditools2: DRR051431 vs influenzaA... 13:07:12 [INFO ] ===> Job 96058: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.bam 13:07:12 [INFO ] Running SNV calling with Reditools2: DRR051442 vs influenzaA... 13:07:12 [INFO ] ===> Job 96059: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.bam 13:07:12 [INFO ] Running SNV calling with Reditools2: DRR051450 vs influenzaA... 13:07:12 [INFO ] ===> Job 96060: samtools index ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.bam 13:07:13 [INFO ] ===> Job 96061: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051417_star.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 13:07:13 [INFO ] ===> Job 96062: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051423_star.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 13:07:13 [INFO ] ===> Job 96063: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051428_star.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 13:07:13 [INFO ] ===> Job 96064: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051431_star.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 13:07:13 [INFO ] ===> Job 96065: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051442_star.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 13:07:13 [INFO ] ===> Job 96066: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../influenzaA/2-alignment/pathogen/bam/influenzaA/DRR051450_star.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 13:07:58 [INFO ] Running step callJacusa... 13:07:58 [INFO ] ===> cp ../influenzaA/data/influenzaA/genome.fa ../influenzaA/4-snvCalling/indices 13:07:58 [INFO ] Running SNV calling with JACUSA: DRR051417 vs influenzaA... 13:07:58 [INFO ] ===> Job 96067: ../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_star.bam 13:07:58 [INFO ] Running SNV calling with JACUSA: DRR051423 vs influenzaA... 13:07:58 [INFO ] ===> Job 96068: ../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_star.bam 13:07:58 [INFO ] Running SNV calling with JACUSA: DRR051428 vs influenzaA... 13:07:58 [INFO ] ===> Job 96069: ../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_star.bam 13:07:58 [INFO ] Running SNV calling with JACUSA: DRR051431 vs influenzaA... 13:07:58 [INFO ] ===> Job 96070: ../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_star.bam 13:07:58 [INFO ] Running SNV calling with JACUSA: DRR051442 vs influenzaA... 13:07:58 [INFO ] ===> Job 96071: ../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_star.bam 13:07:58 [INFO ] Running SNV calling with JACUSA: DRR051450 vs influenzaA... 13:07:58 [INFO ] ===> Job 96072: ../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_star.bam 13:08:06 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 13:08:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051417.jacusa.vcf.pre 13:08:06 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 13:08:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051423.jacusa.vcf.pre 13:08:06 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 13:08:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051428.jacusa.vcf.pre 13:08:06 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 13:08:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051431.jacusa.vcf.pre 13:08:06 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 13:08:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051442.jacusa.vcf.pre 13:08:06 [INFO ] ===> mv ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 13:08:06 [INFO ] ===> rm ../influenzaA/4-snvCalling/calling/jacusa/influenzaA/DRR051450.jacusa.vcf.pre 13:08:06 [INFO ] Running step filterSOR... 13:08:06 [INFO ] Analyzing DRR051417...