23:26:48 [INFO ]  Resuming from step hostAlignment...
23:27:11 [INFO ]  ===> fastq-dump
23:27:11 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -version
23:27:13 [INFO ]  ===> samtools
23:27:13 [INFO ]  ===> ../tools/qualimap_v2.2.1/qualimap --version
23:27:16 [INFO ]  ===> ../tools/FastQC/fastqc
23:27:17 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version
23:27:18 [INFO ]  ===> bcftools
23:27:19 [INFO ]  ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar
23:27:19 [INFO ]  ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py
23:27:22 [INFO ]  ===> ../tools/ncbi-magicblast-1.6.0/bin/magicblast -version
23:27:26 [INFO ]  Running step hostAlignment...
23:27:26 [INFO ]  ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa
23:27:41 [INFO ]  Building Magic-BLAST index file for Homo_sapiens_GRCh38...
23:27:41 [INFO ]  Magic-BLAST index for Homo_sapiens_GRCh38 already built.
23:27:41 [INFO ]  Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file...
23:27:41 [INFO ]  ===> Job 96847: ../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_file_sz 1GB 
23:27:41 [INFO ]  Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file...
23:27:41 [INFO ]  ===> Job 96848: ../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_file_sz 1GB 
23:27:41 [INFO ]  Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file...
23:27:41 [INFO ]  ===> Job 96849: ../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_file_sz 1GB 
23:27:41 [INFO ]  Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file...
23:27:41 [INFO ]  ===> Job 96850: ../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_file_sz 1GB 
23:27:41 [INFO ]  Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file...
23:27:42 [INFO ]  ===> Job 96851: ../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_file_sz 1GB 
23:27:42 [INFO ]  Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file...
23:27:42 [INFO ]  ===> Job 96852: ../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_file_sz 1GB 
23:27:42 [INFO ]  Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file...
23:27:42 [INFO ]  ===> Job 96853: ../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_file_sz 1GB 
23:27:42 [INFO ]  Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file...
23:27:42 [INFO ]  ===> Job 96854: ../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_file_sz 1GB 
23:27:42 [INFO ]  Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file...
23:27:42 [INFO ]  ===> Job 96855: ../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_file_sz 1GB 
23:27:52 [INFO ]  Running step removeAligned...
23:27:52 [ERROR]  Alignment against host for run with ID SRR25792492 not found.