02:19:23 [INFO ]  Executing step removeAligned only...
02:19:28 [INFO ]  ===> fastq-dump
02:19:28 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
02:19:28 [INFO ]  ===> samtools
02:19:28 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
02:19:28 [INFO ]  ===> ../tools/FastQC/fastqc
02:19:29 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
02:19:29 [INFO ]  ===> bcftools
02:19:29 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
02:19:30 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
02:19:31 [INFO ]  ===> ../tools/ncbi-magicblast-1.6.0/bin/magicblast -version
02:19:35 [INFO ]  Running step removeAligned...
02:19:35 [INFO ]  ===> Job 97193: 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
02:19:35 [INFO ]  ===> Job 97194: 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
02:19:35 [INFO ]  ===> Job 97195: 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
02:19:35 [INFO ]  ===> Job 97196: 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
02:19:36 [INFO ]  ===> Job 97197: 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
02:19:36 [INFO ]  ===> Job 97198: 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
02:19:36 [INFO ]  ===> Job 97199: 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
02:19:36 [INFO ]  ===> Job 97200: 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
02:19:36 [INFO ]  ===> Job 97201: 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
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792492.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792493.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792494.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792495.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787973.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787974.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787975.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787976.unmapped.fastq
02:20:37 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787977.unmapped.fastq