02:30:53 [INFO ] Resuming from step hostAlignment... 02:30:57 [INFO ] ===> fastq-dump 02:30:57 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 02:30:58 [INFO ] ===> samtools 02:30:58 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 02:30:58 [INFO ] ===> ../tools/FastQC/fastqc 02:30:59 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 02:30:59 [INFO ] ===> bcftools 02:30:59 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 02:31:00 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 02:31:01 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 02:31:02 [INFO ] Running step hostAlignment... 02:31:02 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 02:31:39 [INFO ] Building STAR index file for Homo_sapiens_GRCh38... 02:31:39 [INFO ] ===> Job 97202: STAR --runThreadN 16 --runMode genomeGenerate --genomeSAindexNbases 6 --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --genomeFastaFiles ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa --genomeSAsparseD 1 > ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star.done 02:31:39 [INFO ] Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97203: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25792492_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792492_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792492 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792492Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792492_star.sam 02:31:39 [INFO ] Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97204: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25792493_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792493_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792493 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792493Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792493_star.sam 02:31:39 [INFO ] Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97205: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25792494_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792494_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792494 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792494Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792494_star.sam 02:31:39 [INFO ] Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97206: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25792495_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792495_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792495 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25792495Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792495_star.sam 02:31:39 [INFO ] Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97207: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25787973_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787973_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787973 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787973Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787973_star.sam 02:31:39 [INFO ] Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97208: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25787974_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787974_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787974 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787974Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787974_star.sam 02:31:39 [INFO ] Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97209: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25787975_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787975_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787975 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787975Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787975_star.sam 02:31:39 [INFO ] Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97210: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25787976_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787976_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787976 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787976Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787976_star.sam 02:31:39 [INFO ] Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file... 02:31:39 [INFO ] ===> Job 97211: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../mtuberculosis2/1-quality/fastq/SRR25787977_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787977_2.fastq --genomeDir ../mtuberculosis2/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787977 --outSAMunmapped Within --limitGenomeGenerateRAM 31000000000 && mv ../mtuberculosis2/2-alignment/host/star/Homo_sapiens_GRCh38/SRR25787977Aligned.out.sam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787977_star.sam 04:01:17 [INFO ] Running step removeAligned... 04:01:17 [INFO ] ===> Job 97212: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792492_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792492_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792492_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792492.unmapped.fastq 04:01:17 [INFO ] ===> Job 97213: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792493_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792493_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792493_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792493.unmapped.fastq 04:01:17 [INFO ] ===> Job 97214: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792494_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792494_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792494_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792494.unmapped.fastq 04:01:17 [INFO ] ===> Job 97215: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792495_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792495_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792495_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792495.unmapped.fastq 04:01:17 [INFO ] ===> Job 97216: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787973_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787973_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787973_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787973.unmapped.fastq 04:01:17 [INFO ] ===> Job 97217: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787974_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787974_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787974_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787974.unmapped.fastq 04:01:17 [INFO ] ===> Job 97218: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787975_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787975_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787975_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787975.unmapped.fastq 04:01:17 [INFO ] ===> Job 97219: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787976_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787976_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787976_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787976.unmapped.fastq 04:01:17 [INFO ] ===> Job 97220: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787977_star.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787977_star.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787977_star.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787977.unmapped.fastq