00:23:22 [INFO ] Resuming from step hostAlignment... 00:23:45 [INFO ] ===> fastq-dump 00:23:45 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 00:23:47 [INFO ] ===> samtools 00:23:47 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 00:23:50 [INFO ] ===> ../tools/FastQC/fastqc 00:23:51 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 00:23:52 [INFO ] ===> bcftools 00:23:52 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 00:23:53 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 00:23:55 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 00:23:56 [INFO ] Running step hostAlignment... 00:23:56 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 00:24:39 [INFO ] Building STAR index file for Homo_sapiens_GRCh38... 00:24:39 [INFO ] STAR index for Homo_sapiens_GRCh38 already built. 00:24:39 [INFO ] Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97277: 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 00:24:39 [INFO ] Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97278: 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 00:24:39 [INFO ] Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97279: 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 00:24:39 [INFO ] Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97280: 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 00:24:39 [INFO ] Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97281: 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 00:24:39 [INFO ] Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97282: 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 00:24:39 [INFO ] Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97283: 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 00:24:39 [INFO ] Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97284: 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 00:24:39 [INFO ] Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file... 00:24:39 [INFO ] ===> Job 97285: 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 00:56:17 [INFO ] Running step removeAligned... 00:56:17 [INFO ] ===> Job 97286: 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 00:56:17 [INFO ] ===> Job 97287: 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 00:56:17 [INFO ] ===> Job 97288: 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 00:56:17 [INFO ] ===> Job 97289: 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 00:56:17 [INFO ] ===> Job 97290: 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 00:56:17 [INFO ] ===> Job 97291: 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 00:56:17 [INFO ] ===> Job 97292: 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 00:56:17 [INFO ] ===> Job 97293: 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 00:56:17 [INFO ] ===> Job 97294: 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 01:27:27 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792492.unmapped.fastq 01:46:07 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792493.unmapped.fastq 02:03:34 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792494.unmapped.fastq 02:23:17 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792495.unmapped.fastq 02:41:51 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787973.unmapped.fastq 02:57:17 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787974.unmapped.fastq 03:16:16 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787975.unmapped.fastq 03:36:32 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787976.unmapped.fastq 03:53:46 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787977.unmapped.fastq 03:55:25 [INFO ] Running step pathogenAlignment... 03:55:25 [INFO ] Building Hisat2 index for mycobacteriumTuberculosis... 03:55:25 [INFO ] ===> Job 97307: ../tools/hisat2-2.1.0/hisat2-build -p 16 ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis > ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis_hisat2.done 03:55:25 [INFO ] Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file... 03:55:26 [INFO ] ===> Job 97308: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25792492_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25792492_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792492_hisat2.sam -p 16 03:55:26 [INFO ] Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file... 03:55:27 [INFO ] ===> Job 97309: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25792493_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25792493_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792493_hisat2.sam -p 16 03:55:27 [INFO ] Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file... 03:55:28 [INFO ] ===> Job 97310: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25792494_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25792494_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792494_hisat2.sam -p 16 03:55:28 [INFO ] Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file... 03:55:28 [INFO ] ===> Job 97311: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25792495_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25792495_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792495_hisat2.sam -p 16 03:55:28 [INFO ] Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file... 03:55:29 [INFO ] ===> Job 97312: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787973_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787973_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787973_hisat2.sam -p 16 03:55:29 [INFO ] Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file... 03:55:30 [INFO ] ===> Job 97313: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787974_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787974_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787974_hisat2.sam -p 16 03:55:30 [INFO ] Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file... 03:55:31 [INFO ] ===> Job 97314: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787975_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787975_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787975_hisat2.sam -p 16 03:55:31 [INFO ] Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file... 03:55:32 [INFO ] ===> Job 97315: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787976_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787976_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787976_hisat2.sam -p 16 03:55:32 [INFO ] Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file... 03:55:32 [INFO ] ===> Job 97316: ../tools/hisat2-2.1.0/hisat2 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787977_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787977_2.fastq -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787977_hisat2.sam -p 16 04:04:59 [INFO ] Running step sort... 04:04:59 [INFO ] Sorting run with ID SRR25792492 vs mycobacteriumTuberculosis BAM file... 04:05:00 [INFO ] ===> Job 97317: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792492_hisat2.sam 04:05:01 [INFO ] ===> Job 97318: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam 04:05:01 [INFO ] Sorting run with ID SRR25792493 vs mycobacteriumTuberculosis BAM file... 04:05:02 [INFO ] ===> Job 97319: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792493_hisat2.sam 04:05:02 [INFO ] ===> Job 97320: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam 04:05:02 [INFO ] Sorting run with ID SRR25792494 vs mycobacteriumTuberculosis BAM file... 04:05:03 [INFO ] ===> Job 97321: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792494_hisat2.sam 04:05:04 [INFO ] ===> Job 97322: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam 04:05:04 [INFO ] Sorting run with ID SRR25792495 vs mycobacteriumTuberculosis BAM file... 04:05:05 [INFO ] ===> Job 97323: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792495_hisat2.sam 04:05:06 [INFO ] ===> Job 97324: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam 04:05:06 [INFO ] Sorting run with ID SRR25787973 vs mycobacteriumTuberculosis BAM file... 04:05:07 [INFO ] ===> Job 97325: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787973_hisat2.sam 04:05:08 [INFO ] ===> Job 97326: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam 04:05:08 [INFO ] Sorting run with ID SRR25787974 vs mycobacteriumTuberculosis BAM file... 04:05:09 [INFO ] ===> Job 97327: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787974_hisat2.sam 04:05:10 [INFO ] ===> Job 97328: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam 04:05:10 [INFO ] Sorting run with ID SRR25787975 vs mycobacteriumTuberculosis BAM file... 04:05:10 [INFO ] ===> Job 97329: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787975_hisat2.sam 04:05:11 [INFO ] ===> Job 97330: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam 04:05:11 [INFO ] Sorting run with ID SRR25787976 vs mycobacteriumTuberculosis BAM file... 04:05:12 [INFO ] ===> Job 97331: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787976_hisat2.sam 04:05:13 [INFO ] ===> Job 97332: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam 04:05:13 [INFO ] Sorting run with ID SRR25787977 vs mycobacteriumTuberculosis BAM file... 04:05:14 [INFO ] ===> Job 97333: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787977_hisat2.sam 04:05:14 [INFO ] ===> Job 97334: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam 04:25:47 [INFO ] Running step runQualimap... 04:25:47 [INFO ] Analyzing the alignment of run with ID SRR25792492 vs mycobacteriumTuberculosis... 04:25:48 [INFO ] ===> Job 97335: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792492 -nt 16 04:25:48 [INFO ] Analyzing the alignment of run with ID SRR25792493 vs mycobacteriumTuberculosis... 04:25:49 [INFO ] ===> Job 97336: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792493 -nt 16 04:25:49 [INFO ] Analyzing the alignment of run with ID SRR25792494 vs mycobacteriumTuberculosis... 04:25:50 [INFO ] ===> Job 97337: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792494 -nt 16 04:25:50 [INFO ] Analyzing the alignment of run with ID SRR25792495 vs mycobacteriumTuberculosis... 04:25:51 [INFO ] ===> Job 97338: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792495 -nt 16 04:25:51 [INFO ] Analyzing the alignment of run with ID SRR25787973 vs mycobacteriumTuberculosis... 04:25:51 [INFO ] ===> Job 97339: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787973 -nt 16 04:25:51 [INFO ] Analyzing the alignment of run with ID SRR25787974 vs mycobacteriumTuberculosis... 04:25:52 [INFO ] ===> Job 97340: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787974 -nt 16 04:25:52 [INFO ] Analyzing the alignment of run with ID SRR25787975 vs mycobacteriumTuberculosis... 04:25:53 [INFO ] ===> Job 97341: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787975 -nt 16 04:25:53 [INFO ] Analyzing the alignment of run with ID SRR25787976 vs mycobacteriumTuberculosis... 04:25:54 [INFO ] ===> Job 97342: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787976 -nt 16 04:25:54 [INFO ] Analyzing the alignment of run with ID SRR25787977 vs mycobacteriumTuberculosis... 04:25:55 [INFO ] ===> Job 97343: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787977 -nt 16 05:16:28 [INFO ] Running step discardHighError... 05:16:28 [INFO ] Discarding high error runs... 05:16:28 [INFO ] No runs were discarded. 05:16:28 [INFO ] Running step callReditools... 05:16:28 [INFO ] ===> cp ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/ 05:16:29 [INFO ] Building Samtools index file for mycobacteriumTuberculosis... 05:16:29 [INFO ] ===> Job 97344: samtools faidx ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/mycobacteriumTuberculosis_faidx.done 05:16:29 [INFO ] Running SNV calling with Reditools2: SRR25792492 vs mycobacteriumTuberculosis... 05:16:30 [INFO ] ===> Job 97345: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam 05:16:30 [INFO ] Running SNV calling with Reditools2: SRR25792493 vs mycobacteriumTuberculosis... 05:16:31 [INFO ] ===> Job 97346: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam 05:16:31 [INFO ] Running SNV calling with Reditools2: SRR25792494 vs mycobacteriumTuberculosis... 05:16:32 [INFO ] ===> Job 97347: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam 05:16:32 [INFO ] Running SNV calling with Reditools2: SRR25792495 vs mycobacteriumTuberculosis... 05:16:32 [INFO ] ===> Job 97348: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam 05:16:32 [INFO ] Running SNV calling with Reditools2: SRR25787973 vs mycobacteriumTuberculosis... 05:16:33 [INFO ] ===> Job 97349: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam 05:16:33 [INFO ] Running SNV calling with Reditools2: SRR25787974 vs mycobacteriumTuberculosis... 05:16:34 [INFO ] ===> Job 97350: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam 05:16:34 [INFO ] Running SNV calling with Reditools2: SRR25787975 vs mycobacteriumTuberculosis... 05:16:35 [INFO ] ===> Job 97351: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam 05:16:35 [INFO ] Running SNV calling with Reditools2: SRR25787976 vs mycobacteriumTuberculosis... 05:16:36 [INFO ] ===> Job 97352: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam 05:16:36 [INFO ] Running SNV calling with Reditools2: SRR25787977 vs mycobacteriumTuberculosis... 05:16:37 [INFO ] ===> Job 97353: samtools index ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam 05:17:10 [INFO ] ===> Job 97354: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792492.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792492.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:11 [INFO ] ===> Job 97355: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792493.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792493.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:12 [INFO ] ===> Job 97356: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792494.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792494.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:13 [INFO ] ===> Job 97357: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25792495.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25792495.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:14 [INFO ] ===> Job 97358: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787973.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787973.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:14 [INFO ] ===> Job 97359: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787974.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787974.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:16 [INFO ] ===> Job 97360: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787975.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787975.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:16 [INFO ] ===> Job 97361: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787976.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787976.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10 05:17:17 [INFO ] ===> Job 97362: ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py -c -f ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam -r ../mtuberculosis2/4-snvCalling/indices/mycobacteriumTuberculosis/genome.fa -m ../mtuberculosis2/4-snvCalling/homopol/mycobacteriumTuberculosis/SRR25787977.homopol.txt -o ../mtuberculosis2/4-snvCalling/calling/reditools/mycobacteriumTuberculosis/SRR25787977.reditools.txt -q 25 -bq 35 -S -s 0 -os 4 -mbp 10 -Mbp 10