22:03:34 [INFO ] ===> fastq-dump 22:03:34 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 22:03:34 [INFO ] ===> samtools 22:03:34 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 22:03:35 [INFO ] ===> ../tools/FastQC/fastqc 22:03:35 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 22:03:36 [INFO ] ===> bcftools 22:03:36 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 22:03:36 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 22:03:38 [INFO ] ===> ../tools/ncbi-magicblast-1.6.0/bin/magicblast -version 22:03:47 [INFO ] 9 experiments found for project PRJNA1010683. 22:03:57 [INFO ] Downloading SRR25792492... 22:03:57 [INFO ] ===> prefetch SRR25792492 --output-directory ../mtuberculosis2/data/sra 22:05:22 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25792492 --outdir ../mtuberculosis2/data/fastq --split-3 22:06:01 [INFO ] Downloading SRR25792493... 22:06:01 [INFO ] ===> prefetch SRR25792493 --output-directory ../mtuberculosis2/data/sra 22:07:17 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25792493 --outdir ../mtuberculosis2/data/fastq --split-3 22:07:47 [INFO ] Downloading SRR25792494... 22:07:47 [INFO ] ===> prefetch SRR25792494 --output-directory ../mtuberculosis2/data/sra 22:09:04 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25792494 --outdir ../mtuberculosis2/data/fastq --split-3 22:09:33 [INFO ] Downloading SRR25792495... 22:09:33 [INFO ] ===> prefetch SRR25792495 --output-directory ../mtuberculosis2/data/sra 22:10:54 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25792495 --outdir ../mtuberculosis2/data/fastq --split-3 22:11:32 [INFO ] Downloading SRR25787973... 22:11:32 [INFO ] ===> prefetch SRR25787973 --output-directory ../mtuberculosis2/data/sra 22:12:53 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25787973 --outdir ../mtuberculosis2/data/fastq --split-3 22:13:33 [INFO ] Downloading SRR25787974... 22:13:33 [INFO ] ===> prefetch SRR25787974 --output-directory ../mtuberculosis2/data/sra 22:14:32 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25787974 --outdir ../mtuberculosis2/data/fastq --split-3 22:14:56 [INFO ] Downloading SRR25787975... 22:14:56 [INFO ] ===> prefetch SRR25787975 --output-directory ../mtuberculosis2/data/sra 22:16:14 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25787975 --outdir ../mtuberculosis2/data/fastq --split-3 22:16:55 [INFO ] Downloading SRR25787976... 22:16:55 [INFO ] ===> prefetch SRR25787976 --output-directory ../mtuberculosis2/data/sra 22:18:16 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25787976 --outdir ../mtuberculosis2/data/fastq --split-3 22:18:52 [INFO ] Downloading SRR25787977... 22:18:52 [INFO ] ===> prefetch SRR25787977 --output-directory ../mtuberculosis2/data/sra 22:20:01 [INFO ] ===> fasterq-dump ../mtuberculosis2/data/sra/SRR25787977 --outdir ../mtuberculosis2/data/fastq --split-3 22:20:31 [INFO ] ===> rm -r ../mtuberculosis2/data/sra 22:20:31 [INFO ] Running step runFastQC... 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25792492_1.fastq ../mtuberculosis2/data/fastq/SRR25792492_2.fastq... 22:20:31 [INFO ] ===> Job 96789: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25792492_1.fastq ../mtuberculosis2/data/fastq/SRR25792492_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25792493_1.fastq ../mtuberculosis2/data/fastq/SRR25792493_2.fastq... 22:20:31 [INFO ] ===> Job 96790: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25792493_1.fastq ../mtuberculosis2/data/fastq/SRR25792493_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25792494_1.fastq ../mtuberculosis2/data/fastq/SRR25792494_2.fastq... 22:20:31 [INFO ] ===> Job 96791: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25792494_1.fastq ../mtuberculosis2/data/fastq/SRR25792494_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25792495_1.fastq ../mtuberculosis2/data/fastq/SRR25792495_2.fastq... 22:20:31 [INFO ] ===> Job 96792: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25792495_1.fastq ../mtuberculosis2/data/fastq/SRR25792495_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25787973_1.fastq ../mtuberculosis2/data/fastq/SRR25787973_2.fastq... 22:20:31 [INFO ] ===> Job 96793: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25787973_1.fastq ../mtuberculosis2/data/fastq/SRR25787973_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25787974_1.fastq ../mtuberculosis2/data/fastq/SRR25787974_2.fastq... 22:20:31 [INFO ] ===> Job 96794: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25787974_1.fastq ../mtuberculosis2/data/fastq/SRR25787974_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25787975_1.fastq ../mtuberculosis2/data/fastq/SRR25787975_2.fastq... 22:20:31 [INFO ] ===> Job 96795: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25787975_1.fastq ../mtuberculosis2/data/fastq/SRR25787975_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25787976_1.fastq ../mtuberculosis2/data/fastq/SRR25787976_2.fastq... 22:20:31 [INFO ] ===> Job 96796: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25787976_1.fastq ../mtuberculosis2/data/fastq/SRR25787976_2.fastq 22:20:31 [INFO ] Analyzing the quality of ../mtuberculosis2/data/fastq/SRR25787977_1.fastq ../mtuberculosis2/data/fastq/SRR25787977_2.fastq... 22:20:31 [INFO ] ===> Job 96797: ../tools/FastQC/fastqc --extract -t 16 -o ../mtuberculosis2/1-quality/fastqc/ -q ../mtuberculosis2/data/fastq/SRR25787977_1.fastq ../mtuberculosis2/data/fastq/SRR25787977_2.fastq 22:25:54 [INFO ] ===> rm -r ../mtuberculosis2/1-quality/fastqctmp 22:25:54 [INFO ] Running step cropLowQuality... 22:25:54 [INFO ] Cropping SRR25792492_1.fastq and SRR25792492_2.fastq... 22:25:54 [INFO ] ===> Job 96824: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25792492_1.fastq ../mtuberculosis2/data/fastq/SRR25792492_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792492_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792492_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25792492_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792492_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25792493_1.fastq and SRR25792493_2.fastq... 22:25:54 [INFO ] ===> Job 96825: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25792493_1.fastq ../mtuberculosis2/data/fastq/SRR25792493_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792493_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792493_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25792493_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792493_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25792494_1.fastq and SRR25792494_2.fastq... 22:25:54 [INFO ] ===> Job 96826: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25792494_1.fastq ../mtuberculosis2/data/fastq/SRR25792494_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792494_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792494_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25792494_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792494_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25792495_1.fastq and SRR25792495_2.fastq... 22:25:54 [INFO ] ===> Job 96827: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25792495_1.fastq ../mtuberculosis2/data/fastq/SRR25792495_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792495_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25792495_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25792495_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25792495_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25787973_1.fastq and SRR25787973_2.fastq... 22:25:54 [INFO ] ===> Job 96828: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25787973_1.fastq ../mtuberculosis2/data/fastq/SRR25787973_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787973_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787973_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25787973_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787973_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25787974_1.fastq and SRR25787974_2.fastq... 22:25:54 [INFO ] ===> Job 96829: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25787974_1.fastq ../mtuberculosis2/data/fastq/SRR25787974_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787974_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787974_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25787974_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787974_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25787975_1.fastq and SRR25787975_2.fastq... 22:25:54 [INFO ] ===> Job 96830: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25787975_1.fastq ../mtuberculosis2/data/fastq/SRR25787975_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787975_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787975_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25787975_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787975_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25787976_1.fastq and SRR25787976_2.fastq... 22:25:54 [INFO ] ===> Job 96831: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25787976_1.fastq ../mtuberculosis2/data/fastq/SRR25787976_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787976_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787976_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25787976_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787976_2.fastq.unpaired CROP:100 22:25:54 [INFO ] Cropping SRR25787977_1.fastq and SRR25787977_2.fastq... 22:25:54 [INFO ] ===> Job 96832: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../mtuberculosis2/data/fastq/SRR25787977_1.fastq ../mtuberculosis2/data/fastq/SRR25787977_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787977_1.fastq ../mtuberculosis2/1-quality/fastq/SRR25787977_1.fastq.unpaired ../mtuberculosis2/1-quality/fastq/SRR25787977_2.fastq ../mtuberculosis2/1-quality/fastq/SRR25787977_2.fastq.unpaired CROP:100 22:49:47 [INFO ] Running step hostAlignment... 22:49:47 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../mtuberculosis2/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 22:50:01 [INFO ] Building Magic-BLAST index file for Homo_sapiens_GRCh38... 22:50:01 [INFO ] ===> Job 96837: ../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_intron_length 500000 > ../mtuberculosis2/2-alignment/host/indices/magicblast/Homo_sapiens_GRCh38_magicblast.done 22:50:01 [INFO ] Mapping SRR25792492_1.fastq and SRR25792492_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96838: ../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 22:50:01 [INFO ] Mapping SRR25792493_1.fastq and SRR25792493_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96839: ../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 22:50:01 [INFO ] Mapping SRR25792494_1.fastq and SRR25792494_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96840: ../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 22:50:01 [INFO ] Mapping SRR25792495_1.fastq and SRR25792495_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96841: ../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 22:50:01 [INFO ] Mapping SRR25787973_1.fastq and SRR25787973_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96842: ../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 22:50:01 [INFO ] Mapping SRR25787974_1.fastq and SRR25787974_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96843: ../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 22:50:01 [INFO ] Mapping SRR25787975_1.fastq and SRR25787975_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96844: ../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 22:50:01 [INFO ] Mapping SRR25787976_1.fastq and SRR25787976_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96845: ../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 22:50:01 [INFO ] Mapping SRR25787977_1.fastq and SRR25787977_2.fastq to the reference file... 22:50:01 [INFO ] ===> Job 96846: ../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 22:50:08 [INFO ] Running step removeAligned... 22:50:08 [ERROR] Alignment against host for run with ID SRR25792492 not found.