23:45:26 [INFO ] Resuming from step hostAlignment... 23:45:30 [INFO ] ===> fastq-dump 23:45:31 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 23:45:31 [INFO ] ===> samtools 23:45:31 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 23:45:31 [INFO ] ===> ../tools/FastQC/fastqc 23:45:32 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 23:45:32 [INFO ] ===> bcftools 23:45:32 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 23:45:33 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 23:45:34 [INFO ] ===> ../tools/ncbi-magicblast-1.6.0/bin/magicblast -version 23:45:39 [INFO ] Running step hostAlignment... 23:45:39 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 23:45:48 [INFO ] Building Magic-BLAST index file for Homo_sapiens_GRCh38... 23:45:48 [INFO ] ===> Job 96876: ../tools/ncbi-magicblast-1.6.0/bin//makeblastdb -in ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa -out ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -parse_seqids -dbtype nucl -max_file_sz 1GB > ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38_magicblast.done 23:45:48 [INFO ] Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96877: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25792492_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25792492_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792492_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96878: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25792493_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25792493_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792493_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96879: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25792494_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25792494_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792494_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96880: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25792495_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25792495_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792495_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96881: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25787973_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25787973_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787973_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96882: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25787974_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25787974_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787974_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96883: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25787975_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25787975_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787975_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96884: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25787976_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25787976_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787976_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 23:45:48 [INFO ] Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file... 23:45:48 [INFO ] ===> Job 96885: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38 -paired -query ../mtuberculosis2/1-quality/fastq/SRR25787977_1.fastq -query_mate ../mtuberculosis2/1-quality/fastq/SRR25787977_2.fastq -out ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787977_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:41:27 [INFO ] Running step removeAligned... 00:41:27 [INFO ] ===> Job 97016: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792492_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792492_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792492_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792492.unmapped.fastq 00:41:27 [INFO ] ===> Job 97017: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792493_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792493_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792493_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792493.unmapped.fastq 00:41:27 [INFO ] ===> Job 97018: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792494_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792494_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792494_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792494.unmapped.fastq 00:41:27 [INFO ] ===> Job 97019: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792495_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25792495_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25792495_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25792495.unmapped.fastq 00:41:27 [INFO ] ===> Job 97020: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787973_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787973_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787973_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787973.unmapped.fastq 00:41:27 [INFO ] ===> Job 97021: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787974_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787974_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787974_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787974.unmapped.fastq 00:41:27 [INFO ] ===> Job 97022: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787975_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787975_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787975_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787975.unmapped.fastq 00:41:27 [INFO ] ===> Job 97023: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787976_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787976_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787976_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787976.unmapped.fastq 00:41:27 [INFO ] ===> Job 97024: samtools view -f 13 -F 256 -bo ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787977_magicblast.bam ../mtuberculosis2/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR25787977_magicblast.sam && samtools bam2fq ../mtuberculosis2/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR25787977_magicblast.bam > ../mtuberculosis2/2-alignment/host/fastq/SRR25787977.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792492.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792493.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792494.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792495.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787973.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787974.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787975.unmapped.fastq 00:43:06 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787976.unmapped.fastq 00:43:07 [INFO ] ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787977.unmapped.fastq 00:43:07 [INFO ] Running step pathogenAlignment... 00:43:07 [INFO ] Building Magic-BLAST index file for mycobacteriumTuberculosis... 00:43:07 [INFO ] ===> Job 97031: ../tools/ncbi-magicblast-1.6.0/bin//makeblastdb -in ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa -out ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -parse_seqids -dbtype nucl -max_file_sz 1GB > ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis_magicblast.done 00:43:07 [INFO ] Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97032: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25792492_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25792492_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792492_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97033: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25792493_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25792493_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792493_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97034: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25792494_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25792494_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792494_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97035: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25792495_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25792495_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792495_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97036: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25787973_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25787973_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787973_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97037: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25787974_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25787974_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787974_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97038: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25787975_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25787975_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787975_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97039: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25787976_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25787976_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787976_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:07 [INFO ] Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file... 00:43:07 [INFO ] ===> Job 97040: ../tools/ncbi-magicblast-1.6.0/bin//magicblast -db ../mtuberculosis2/2-alignment/pathogen/indices/magicblast/mycobacteriumTuberculosis -paired -query ../mtuberculosis2/2-alignment/host/fastq/SRR25787977_1.fastq -query_mate ../mtuberculosis2/2-alignment/host/fastq/SRR25787977_2.fastq -out ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787977_magicblast.sam -infmt fastq -num_threads 16 -max_intron_length 500000 00:43:20 [INFO ] Running step sort... 00:43:20 [INFO ] Sorting run with ID SRR25792492 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97041: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792492_magicblast.sam 00:43:20 [INFO ] ===> Job 97042: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_magicblast.bam 00:43:20 [INFO ] Sorting run with ID SRR25792493 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97043: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792493_magicblast.sam 00:43:20 [INFO ] ===> Job 97044: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_magicblast.bam 00:43:20 [INFO ] Sorting run with ID SRR25792494 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97045: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792494_magicblast.sam 00:43:20 [INFO ] ===> Job 97046: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_magicblast.bam 00:43:20 [INFO ] Sorting run with ID SRR25792495 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97047: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792495_magicblast.sam 00:43:20 [INFO ] ===> Job 97048: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_magicblast.bam 00:43:20 [INFO ] Sorting run with ID SRR25787973 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97049: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787973_magicblast.sam 00:43:20 [INFO ] ===> Job 97050: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_magicblast.bam 00:43:20 [INFO ] Sorting run with ID SRR25787974 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97051: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787974_magicblast.sam 00:43:20 [INFO ] ===> Job 97052: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_magicblast.bam 00:43:20 [INFO ] Sorting run with ID SRR25787975 vs mycobacteriumTuberculosis BAM file... 00:43:20 [INFO ] ===> Job 97053: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787975_magicblast.sam 00:43:21 [INFO ] ===> Job 97054: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_magicblast.bam 00:43:21 [INFO ] Sorting run with ID SRR25787976 vs mycobacteriumTuberculosis BAM file... 00:43:21 [INFO ] ===> Job 97055: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787976_magicblast.sam 00:43:21 [INFO ] ===> Job 97056: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_magicblast.bam 00:43:21 [INFO ] Sorting run with ID SRR25787977 vs mycobacteriumTuberculosis BAM file... 00:43:21 [INFO ] ===> Job 97057: samtools sort -O BAM -o ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_magicblast.sorted.bam ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25787977_magicblast.sam 00:43:21 [INFO ] ===> Job 97058: samtools calmd -b ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_magicblast.sorted.bam ../mtuberculosis2/data/mycobacteriumTuberculosis/genome.fa > ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_magicblast.bam 00:43:23 [INFO ] Running step runQualimap... 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25792492 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97059: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792492 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25792493 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97060: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792493 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25792494 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97061: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792494 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25792495 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97062: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792495 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25787973 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97063: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787973 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25787974 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97064: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787974 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25787975 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97065: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787975 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25787976 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97066: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787976 -nt 16 00:43:23 [INFO ] Analyzing the alignment of run with ID SRR25787977 vs mycobacteriumTuberculosis... 00:43:23 [INFO ] ===> Job 97067: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_magicblast.bam -outdir ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787977 -nt 16 00:43:34 [INFO ] Running step discardHighError... 00:43:34 [INFO ] Discarding high error runs... 00:43:34 [ERROR] Qualimap results for run with ID SRR25792492 against pathogen reference mycobacteriumTuberculosis not found.