03:41:20 [INFO ] Resuming from step removeAligned... 03:41:47 [INFO ] ===> fastq-dump 03:41:47 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 03:41:49 [INFO ] ===> samtools 03:41:49 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 03:41:52 [INFO ] ===> ../tools/FastQC/fastqc 03:41:53 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 03:41:54 [INFO ] ===> bcftools 03:41:55 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 03:41:55 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 03:41:59 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 03:41:59 [INFO ] Running step removeAligned... 03:41:59 [INFO ] ===> Job 96578: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR950197_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR950197_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR950197_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR950197.unmapped.fastq 03:41:59 [INFO ] ===> Job 96579: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR950198_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR950198_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR950198_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR950198.unmapped.fastq 03:41:59 [INFO ] ===> Job 96580: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949916_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949916_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949916_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR949916.unmapped.fastq 03:41:59 [INFO ] ===> Job 96581: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR950093_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR950093_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR950093_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR950093.unmapped.fastq 03:41:59 [INFO ] ===> Job 96582: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949601_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949601_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949601_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR949601.unmapped.fastq 03:41:59 [INFO ] ===> Job 96583: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949624_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949624_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949624_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR949624.unmapped.fastq 03:41:59 [INFO ] ===> Job 96584: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949060_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949060_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949060_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR949060.unmapped.fastq 03:41:59 [INFO ] ===> Job 96585: samtools view -f 13 -F 256 -bo ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949270_star.bam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949270_star.sam && samtools bam2fq ../hcapsulatum/2-alignment/host/bam/Homo_sapiens_GRCh38/SRR949270_star.bam > ../hcapsulatum/2-alignment/host/fastq/SRR949270.unmapped.fastq 03:53:02 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR950197.unmapped.fastq 04:02:07 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR950198.unmapped.fastq 04:10:48 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR949916.unmapped.fastq 04:20:55 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR950093.unmapped.fastq 04:28:00 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR949601.unmapped.fastq 04:33:01 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR949624.unmapped.fastq 04:38:24 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR949060.unmapped.fastq 04:44:23 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR949270.unmapped.fastq 04:44:49 [INFO ] Running step pathogenAlignment... 04:44:49 [INFO ] Building Hisat2 index for genome... 04:44:49 [INFO ] ===> Job 96586: ../tools/hisat2-2.1.0/hisat2-build -p 16 ../hcapsulatum/data/genome/genome.fa ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome > ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome_hisat2.done 04:44:49 [INFO ] Mapping SRR950197_1.fastq and SRR950197_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96587: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR950197_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR950197_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR950197_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR950198_1.fastq and SRR950198_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96588: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR950198_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR950198_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR950198_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR949916_1.fastq and SRR949916_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96589: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR949916_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949916_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949916_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR950093_1.fastq and SRR950093_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96590: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR950093_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR950093_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR950093_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR949601_1.fastq and SRR949601_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96591: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR949601_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949601_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949601_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR949624_1.fastq and SRR949624_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96592: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR949624_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949624_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949624_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR949060_1.fastq and SRR949060_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96593: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR949060_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949060_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949060_hisat2.sam -p 16 04:44:49 [INFO ] Mapping SRR949270_1.fastq and SRR949270_2.fastq to the reference file... 04:44:49 [INFO ] ===> Job 96594: ../tools/hisat2-2.1.0/hisat2 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -1 ../hcapsulatum/2-alignment/host/fastq/SRR949270_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949270_2.fastq -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949270_hisat2.sam -p 16 04:48:30 [INFO ] Running step sort... 04:48:30 [INFO ] Sorting run with ID SRR950197 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96595: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR950197_hisat2.sam 04:48:30 [INFO ] ===> Job 96596: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR950198 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96597: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR950198_hisat2.sam 04:48:30 [INFO ] ===> Job 96598: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR949916 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96599: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949916_hisat2.sam 04:48:30 [INFO ] ===> Job 96600: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR950093 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96601: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR950093_hisat2.sam 04:48:30 [INFO ] ===> Job 96602: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR949601 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96603: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949601_hisat2.sam 04:48:30 [INFO ] ===> Job 96604: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR949624 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96605: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949624_hisat2.sam 04:48:30 [INFO ] ===> Job 96606: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR949060 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96607: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949060_hisat2.sam 04:48:30 [INFO ] ===> Job 96608: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam 04:48:30 [INFO ] Sorting run with ID SRR949270 vs genome BAM file... 04:48:30 [INFO ] ===> Job 96609: samtools sort -O BAM -o ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.sorted.bam ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949270_hisat2.sam 04:48:30 [INFO ] ===> Job 96610: samtools calmd -b ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.sorted.bam ../hcapsulatum/data/genome/genome.fa > ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam 04:53:49 [INFO ] Running step runQualimap... 04:53:49 [INFO ] Analyzing the alignment of run with ID SRR950197 vs genome... 04:53:49 [INFO ] ===> Job 96611: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR950197 -nt 16 04:53:49 [INFO ] Analyzing the alignment of run with ID SRR950198 vs genome... 04:53:49 [INFO ] ===> Job 96612: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR950198 -nt 16 04:53:49 [INFO ] Analyzing the alignment of run with ID SRR949916 vs genome... 04:53:49 [INFO ] ===> Job 96613: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR949916 -nt 16 04:53:49 [INFO ] Analyzing the alignment of run with ID SRR950093 vs genome... 04:53:50 [INFO ] ===> Job 96614: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR950093 -nt 16 04:53:50 [INFO ] Analyzing the alignment of run with ID SRR949601 vs genome... 04:53:50 [INFO ] ===> Job 96615: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR949601 -nt 16 04:53:50 [INFO ] Analyzing the alignment of run with ID SRR949624 vs genome... 04:53:50 [INFO ] ===> Job 96616: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR949624 -nt 16 04:53:50 [INFO ] Analyzing the alignment of run with ID SRR949060 vs genome... 04:53:50 [INFO ] ===> Job 96617: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR949060 -nt 16 04:53:50 [INFO ] Analyzing the alignment of run with ID SRR949270 vs genome... 04:53:50 [INFO ] ===> Job 96618: ../tools/qualimap_v2.2.1/qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam -outdir ../hcapsulatum/3-qualimap/genome/SRR949270 -nt 16 04:55:54 [INFO ] Running step discardHighError... 04:55:54 [INFO ] Discarding high error runs... 04:55:54 [INFO ] No runs were discarded. 04:55:54 [INFO ] Running step callReditools...