00:59:39 [INFO ] ===> cp ../sampleData/pathogenRef/influenzaA/influenzaA/influenzaA.fa ../influenzaA/data/influenzaA/genome.fa 00:59:39 [INFO ] ===> cp ../sampleData/pathogenRef/influenzaA/influenzaA/influenzaA.fa ../influenzaA/data/influenzaA/genes.gbk 00:59:39 [INFO ] ===> cp ../sampleData/pathogenRef/influenzaA/influenzaA/influenzaA.fa ../influenzaA/data/influenzaA/protein.fa 00:59:43 [INFO ] ===> fastq-dump 00:59:44 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 00:59:45 [INFO ] ===> samtools 00:59:45 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 00:59:48 [INFO ] ===> ../tools/FastQC/fastqc 00:59:49 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 00:59:50 [INFO ] ===> bcftools 00:59:51 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 00:59:51 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 00:59:54 [INFO ] ===> STAR 00:59:54 [INFO ] Downloading DRR051417... 00:59:54 [INFO ] ===> prefetch DRR051417 --output-directory ../influenzaA/data/sra 01:00:04 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051417 --outdir ../influenzaA/data/fastq --split-3 01:00:06 [INFO ] Downloading DRR051423... 01:00:06 [INFO ] ===> prefetch DRR051423 --output-directory ../influenzaA/data/sra 01:00:14 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051423 --outdir ../influenzaA/data/fastq --split-3 01:00:16 [INFO ] Downloading DRR051428... 01:00:16 [INFO ] ===> prefetch DRR051428 --output-directory ../influenzaA/data/sra 01:00:24 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051428 --outdir ../influenzaA/data/fastq --split-3 01:00:25 [INFO ] Downloading DRR051431... 01:00:25 [INFO ] ===> prefetch DRR051431 --output-directory ../influenzaA/data/sra 01:00:33 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051431 --outdir ../influenzaA/data/fastq --split-3 01:00:34 [INFO ] Downloading DRR051442... 01:00:34 [INFO ] ===> prefetch DRR051442 --output-directory ../influenzaA/data/sra 01:00:41 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051442 --outdir ../influenzaA/data/fastq --split-3 01:00:42 [INFO ] ===> cat ../influenzaA/data/fastq/DRR051442.fastq >> ../influenzaA/data/fastq/DRR051442.fastq 01:00:42 [INFO ] Downloading DRR051444... 01:00:42 [INFO ] ===> prefetch DRR051444 --output-directory ../influenzaA/data/sra 01:00:49 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051444 --outdir ../influenzaA/data/fastq --split-3 01:00:50 [INFO ] ===> cat ../influenzaA/data/fastq/DRR051444.fastq >> ../influenzaA/data/fastq/DRR051444.fastq 01:00:50 [INFO ] Downloading DRR051450... 01:00:50 [INFO ] ===> prefetch DRR051450 --output-directory ../influenzaA/data/sra 01:01:09 [INFO ] ===> fasterq-dump ../influenzaA/data/sra/DRR051450 --outdir ../influenzaA/data/fastq --split-3 01:01:11 [INFO ] ===> rm -r ../influenzaA/data/sra 01:01:11 [INFO ] Running step runFastQC... 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051417_1.fastq ../influenzaA/data/fastq/DRR051417_2.fastq... 01:01:11 [INFO ] ===> Job 95987: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051417_1.fastq ../influenzaA/data/fastq/DRR051417_2.fastq 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051423_1.fastq ../influenzaA/data/fastq/DRR051423_2.fastq... 01:01:11 [INFO ] ===> Job 95988: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051423_1.fastq ../influenzaA/data/fastq/DRR051423_2.fastq 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051428_1.fastq ../influenzaA/data/fastq/DRR051428_2.fastq... 01:01:11 [INFO ] ===> Job 95989: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051428_1.fastq ../influenzaA/data/fastq/DRR051428_2.fastq 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051431_1.fastq ../influenzaA/data/fastq/DRR051431_2.fastq... 01:01:11 [INFO ] ===> Job 95990: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051431_1.fastq ../influenzaA/data/fastq/DRR051431_2.fastq 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051442.fastq... 01:01:11 [INFO ] ===> Job 95991: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051442.fastq 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051444.fastq... 01:01:11 [INFO ] ===> Job 95992: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051444.fastq 01:01:11 [INFO ] Analyzing the quality of ../influenzaA/data/fastq/DRR051450_1.fastq ../influenzaA/data/fastq/DRR051450_2.fastq... 01:01:11 [INFO ] ===> Job 95993: ../tools/FastQC/fastqc --extract -t 16 -o ../influenzaA/1-quality/fastqc/ -q ../influenzaA/data/fastq/DRR051450_1.fastq ../influenzaA/data/fastq/DRR051450_2.fastq 01:01:26 [INFO ] ===> rm -r ../influenzaA/1-quality/fastqctmp 01:01:26 [INFO ] Running step cropLowQuality... 01:01:26 [INFO ] Cropping DRR051417_1.fastq and DRR051417_2.fastq... 01:01:26 [INFO ] ===> Job 95994: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../influenzaA/data/fastq/DRR051417_1.fastq ../influenzaA/data/fastq/DRR051417_2.fastq ../influenzaA/1-quality/fastq/DRR051417_1.fastq ../influenzaA/1-quality/fastq/DRR051417_1.fastq.unpaired ../influenzaA/1-quality/fastq/DRR051417_2.fastq ../influenzaA/1-quality/fastq/DRR051417_2.fastq.unpaired CROP:100 01:01:26 [INFO ] Cropping DRR051423_1.fastq and DRR051423_2.fastq... 01:01:26 [INFO ] ===> Job 95995: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../influenzaA/data/fastq/DRR051423_1.fastq ../influenzaA/data/fastq/DRR051423_2.fastq ../influenzaA/1-quality/fastq/DRR051423_1.fastq ../influenzaA/1-quality/fastq/DRR051423_1.fastq.unpaired ../influenzaA/1-quality/fastq/DRR051423_2.fastq ../influenzaA/1-quality/fastq/DRR051423_2.fastq.unpaired CROP:100 01:01:26 [INFO ] Cropping DRR051428_1.fastq and DRR051428_2.fastq... 01:01:26 [INFO ] ===> Job 95996: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../influenzaA/data/fastq/DRR051428_1.fastq ../influenzaA/data/fastq/DRR051428_2.fastq ../influenzaA/1-quality/fastq/DRR051428_1.fastq ../influenzaA/1-quality/fastq/DRR051428_1.fastq.unpaired ../influenzaA/1-quality/fastq/DRR051428_2.fastq ../influenzaA/1-quality/fastq/DRR051428_2.fastq.unpaired CROP:100 01:01:26 [INFO ] Cropping DRR051431_1.fastq and DRR051431_2.fastq... 01:01:26 [INFO ] ===> Job 95997: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../influenzaA/data/fastq/DRR051431_1.fastq ../influenzaA/data/fastq/DRR051431_2.fastq ../influenzaA/1-quality/fastq/DRR051431_1.fastq ../influenzaA/1-quality/fastq/DRR051431_1.fastq.unpaired ../influenzaA/1-quality/fastq/DRR051431_2.fastq ../influenzaA/1-quality/fastq/DRR051431_2.fastq.unpaired CROP:100 01:01:26 [INFO ] Cropping DRR051442.fastq... 01:01:26 [INFO ] ===> Job 95998: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar SE ../influenzaA/data/fastq/DRR051442.fastq ../influenzaA/1-quality/fastq/DRR051442.fastq CROP:100 01:01:26 [INFO ] Cropping DRR051444.fastq... 01:01:26 [INFO ] ===> Job 95999: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar SE ../influenzaA/data/fastq/DRR051444.fastq ../influenzaA/1-quality/fastq/DRR051444.fastq CROP:100 01:01:26 [INFO ] Cropping DRR051450_1.fastq and DRR051450_2.fastq... 01:01:26 [INFO ] ===> Job 96000: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../influenzaA/data/fastq/DRR051450_1.fastq ../influenzaA/data/fastq/DRR051450_2.fastq ../influenzaA/1-quality/fastq/DRR051450_1.fastq ../influenzaA/1-quality/fastq/DRR051450_1.fastq.unpaired ../influenzaA/1-quality/fastq/DRR051450_2.fastq ../influenzaA/1-quality/fastq/DRR051450_2.fastq.unpaired CROP:100 01:01:49 [INFO ] Running step hostAlignment... 01:01:49 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 01:02:25 [INFO ] Building STAR index file for Homo_sapiens_GRCh38... 01:02:25 [INFO ] ===> Job 96001: STAR --runThreadN 16 --runMode genomeGenerate --genomeSAindexNbases 6 --genomeDir ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star --genomeFastaFiles ../influenzaA/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa --genomeSAsparseD 1 > ../influenzaA/2-alignment/host/indices/Homo_sapiens_GRCh38_star.done 01:02:25 [INFO ] Mapping DRR051417_1.fastq and DRR051417_2.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96002: 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 01:02:25 [INFO ] Mapping DRR051423_1.fastq and DRR051423_2.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96003: 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 01:02:25 [INFO ] Mapping DRR051428_1.fastq and DRR051428_2.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96004: 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 01:02:25 [INFO ] Mapping DRR051431_1.fastq and DRR051431_2.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96005: 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 01:02:25 [INFO ] Mapping DRR051442.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96006: 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 01:02:25 [INFO ] Mapping DRR051444.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96007: 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 01:02:25 [INFO ] Mapping DRR051450_1.fastq and DRR051450_2.fastq to the reference file... 01:02:25 [INFO ] ===> Job 96008: 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 02:10:04 [INFO ] Running step removeAligned... 02:10:04 [INFO ] ===> Job 96009: 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 02:10:04 [ERROR] Alignment against host for run with ID DRR051423 not found.