02:17:10 [INFO ]  Resuming from step removeAligned...
02:17:14 [INFO ]  ===> fastq-dump
02:17:15 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
02:17:16 [INFO ]  ===> samtools
02:17:16 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
02:17:17 [INFO ]  ===> ../tools/FastQC/fastqc
02:17:18 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
02:17:19 [INFO ]  ===> bcftools
02:17:19 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
02:17:19 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
02:17:22 [INFO ]  ===> ../tools/ncbi-magicblast-1.6.0/bin/magicblast -version
02:17:23 [INFO ]  Running step removeAligned...
02:17:23 [INFO ]  ===> Job 97184: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97185: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97186: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97187: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97188: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97189: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97190: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97191: samtools view -f 13 -F 256  -F 12 -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
02:17:23 [INFO ]  ===> Job 97192: samtools view -f 13 -F 256  -F 12 -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
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792492.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25792492 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792493.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25792493 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792494.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25792494 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25792495.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25792495 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787973.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25787973 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787974.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25787974 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787975.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25787975 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787976.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25787976 aligned to the host. Discarding file...
02:18:24 [INFO ]  ===> rm ../mtuberculosis2/2-alignment/host/fastq/SRR25787977.unmapped.fastq
02:18:24 [INFO ]  All sequences from run with ID SRR25787977 aligned to the host. Discarding file...
02:18:24 [ERROR]  All runs were discarded.