01:28:27 [INFO ] ===> cp ../sampleData/pathogenRef/histoplasmaCapsulatum/histoplasmaCapsulatum/genome.fa ../hcapsulatum/data/genome/genome.fa 01:28:27 [INFO ] ===> cp ../sampleData/pathogenRef/histoplasmaCapsulatum/histoplasmaCapsulatum/genes.gbk ../hcapsulatum/data/genome/genes.gbk 01:28:27 [INFO ] ===> cp ../sampleData/pathogenRef/histoplasmaCapsulatum/histoplasmaCapsulatum/protein.fa ../hcapsulatum/data/genome/protein.fa 01:28:49 [INFO ] ===> fastq-dump 01:28:49 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -version 01:28:50 [INFO ] ===> samtools 01:28:51 [INFO ] ===> ../tools/qualimap_v2.2.1/qualimap --version 01:28:53 [INFO ] ===> ../tools/FastQC/fastqc 01:28:54 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/snpEff/snpEff.jar -version 01:28:55 [INFO ] ===> bcftools 01:28:56 [INFO ] ===> ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar 01:28:56 [INFO ] ===> ../tools/REDItools2/env/bin/python2 ../tools/REDItools2/src/cineca/reditools.py 01:28:59 [INFO ] ===> ../tools/hisat2-2.1.0/hisat2 --version 01:29:04 [INFO ] 4 experiments found for project PRJNA214093. 01:29:05 [INFO ] Downloading SRR950197... 01:29:05 [INFO ] ===> prefetch SRR950197 --output-directory ../hcapsulatum/data/sra 01:29:43 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR950197 --outdir ../hcapsulatum/data/fastq --split-3 01:30:07 [INFO ] Downloading SRR950198... 01:30:07 [INFO ] ===> prefetch SRR950198 --output-directory ../hcapsulatum/data/sra 01:30:44 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR950198 --outdir ../hcapsulatum/data/fastq --split-3 01:30:57 [INFO ] Downloading SRR949916... 01:30:57 [INFO ] ===> prefetch SRR949916 --output-directory ../hcapsulatum/data/sra 01:31:44 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR949916 --outdir ../hcapsulatum/data/fastq --split-3 01:31:58 [INFO ] Downloading SRR950093... 01:31:58 [INFO ] ===> prefetch SRR950093 --output-directory ../hcapsulatum/data/sra 01:32:38 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR950093 --outdir ../hcapsulatum/data/fastq --split-3 01:32:54 [INFO ] Downloading SRR949601... 01:32:54 [INFO ] ===> prefetch SRR949601 --output-directory ../hcapsulatum/data/sra 01:33:17 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR949601 --outdir ../hcapsulatum/data/fastq --split-3 01:33:25 [INFO ] Downloading SRR949624... 01:33:25 [INFO ] ===> prefetch SRR949624 --output-directory ../hcapsulatum/data/sra 01:33:44 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR949624 --outdir ../hcapsulatum/data/fastq --split-3 01:33:51 [INFO ] Downloading SRR949060... 01:33:51 [INFO ] ===> prefetch SRR949060 --output-directory ../hcapsulatum/data/sra 01:34:24 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR949060 --outdir ../hcapsulatum/data/fastq --split-3 01:34:32 [INFO ] Downloading SRR949270... 01:34:32 [INFO ] ===> prefetch SRR949270 --output-directory ../hcapsulatum/data/sra 01:34:53 [INFO ] ===> fasterq-dump ../hcapsulatum/data/sra/SRR949270 --outdir ../hcapsulatum/data/fastq --split-3 01:35:01 [INFO ] ===> rm -r ../hcapsulatum/data/sra 01:35:01 [INFO ] Running step runFastQC... 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR950197_1.fastq ../hcapsulatum/data/fastq/SRR950197_2.fastq... 01:35:01 [INFO ] ===> Job 96545: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR950197_1.fastq ../hcapsulatum/data/fastq/SRR950197_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR950198_1.fastq ../hcapsulatum/data/fastq/SRR950198_2.fastq... 01:35:01 [INFO ] ===> Job 96546: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR950198_1.fastq ../hcapsulatum/data/fastq/SRR950198_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR949916_1.fastq ../hcapsulatum/data/fastq/SRR949916_2.fastq... 01:35:01 [INFO ] ===> Job 96547: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR949916_1.fastq ../hcapsulatum/data/fastq/SRR949916_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR950093_1.fastq ../hcapsulatum/data/fastq/SRR950093_2.fastq... 01:35:01 [INFO ] ===> Job 96548: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR950093_1.fastq ../hcapsulatum/data/fastq/SRR950093_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR949601_1.fastq ../hcapsulatum/data/fastq/SRR949601_2.fastq... 01:35:01 [INFO ] ===> Job 96549: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR949601_1.fastq ../hcapsulatum/data/fastq/SRR949601_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR949624_1.fastq ../hcapsulatum/data/fastq/SRR949624_2.fastq... 01:35:01 [INFO ] ===> Job 96550: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR949624_1.fastq ../hcapsulatum/data/fastq/SRR949624_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR949060_1.fastq ../hcapsulatum/data/fastq/SRR949060_2.fastq... 01:35:01 [INFO ] ===> Job 96551: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR949060_1.fastq ../hcapsulatum/data/fastq/SRR949060_2.fastq 01:35:01 [INFO ] Analyzing the quality of ../hcapsulatum/data/fastq/SRR949270_1.fastq ../hcapsulatum/data/fastq/SRR949270_2.fastq... 01:35:01 [INFO ] ===> Job 96552: ../tools/FastQC/fastqc --extract -t 16 -o ../hcapsulatum/1-quality/fastqc/ -q ../hcapsulatum/data/fastq/SRR949270_1.fastq ../hcapsulatum/data/fastq/SRR949270_2.fastq 01:35:55 [INFO ] ===> rm -r ../hcapsulatum/1-quality/fastqctmp 01:35:55 [INFO ] Running step cropLowQuality... 01:35:55 [INFO ] Cropping SRR950197_1.fastq and SRR950197_2.fastq... 01:35:55 [INFO ] ===> Job 96553: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR950197_1.fastq ../hcapsulatum/data/fastq/SRR950197_2.fastq ../hcapsulatum/1-quality/fastq/SRR950197_1.fastq ../hcapsulatum/1-quality/fastq/SRR950197_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR950197_2.fastq ../hcapsulatum/1-quality/fastq/SRR950197_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR950198_1.fastq and SRR950198_2.fastq... 01:35:55 [INFO ] ===> Job 96554: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR950198_1.fastq ../hcapsulatum/data/fastq/SRR950198_2.fastq ../hcapsulatum/1-quality/fastq/SRR950198_1.fastq ../hcapsulatum/1-quality/fastq/SRR950198_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR950198_2.fastq ../hcapsulatum/1-quality/fastq/SRR950198_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR949916_1.fastq and SRR949916_2.fastq... 01:35:55 [INFO ] ===> Job 96555: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR949916_1.fastq ../hcapsulatum/data/fastq/SRR949916_2.fastq ../hcapsulatum/1-quality/fastq/SRR949916_1.fastq ../hcapsulatum/1-quality/fastq/SRR949916_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR949916_2.fastq ../hcapsulatum/1-quality/fastq/SRR949916_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR950093_1.fastq and SRR950093_2.fastq... 01:35:55 [INFO ] ===> Job 96556: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR950093_1.fastq ../hcapsulatum/data/fastq/SRR950093_2.fastq ../hcapsulatum/1-quality/fastq/SRR950093_1.fastq ../hcapsulatum/1-quality/fastq/SRR950093_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR950093_2.fastq ../hcapsulatum/1-quality/fastq/SRR950093_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR949601_1.fastq and SRR949601_2.fastq... 01:35:55 [INFO ] ===> Job 96557: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR949601_1.fastq ../hcapsulatum/data/fastq/SRR949601_2.fastq ../hcapsulatum/1-quality/fastq/SRR949601_1.fastq ../hcapsulatum/1-quality/fastq/SRR949601_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR949601_2.fastq ../hcapsulatum/1-quality/fastq/SRR949601_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR949624_1.fastq and SRR949624_2.fastq... 01:35:55 [INFO ] ===> Job 96558: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR949624_1.fastq ../hcapsulatum/data/fastq/SRR949624_2.fastq ../hcapsulatum/1-quality/fastq/SRR949624_1.fastq ../hcapsulatum/1-quality/fastq/SRR949624_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR949624_2.fastq ../hcapsulatum/1-quality/fastq/SRR949624_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR949060_1.fastq and SRR949060_2.fastq... 01:35:55 [INFO ] ===> Job 96559: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR949060_1.fastq ../hcapsulatum/data/fastq/SRR949060_2.fastq ../hcapsulatum/1-quality/fastq/SRR949060_1.fastq ../hcapsulatum/1-quality/fastq/SRR949060_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR949060_2.fastq ../hcapsulatum/1-quality/fastq/SRR949060_2.fastq.unpaired CROP:100 01:35:55 [INFO ] Cropping SRR949270_1.fastq and SRR949270_2.fastq... 01:35:55 [INFO ] ===> Job 96560: ../tools/jdk-13.0.2/bin/java -jar ../tools/Trimmomatic-0.39/trimmomatic-0.39.jar PE ../hcapsulatum/data/fastq/SRR949270_1.fastq ../hcapsulatum/data/fastq/SRR949270_2.fastq ../hcapsulatum/1-quality/fastq/SRR949270_1.fastq ../hcapsulatum/1-quality/fastq/SRR949270_1.fastq.unpaired ../hcapsulatum/1-quality/fastq/SRR949270_2.fastq ../hcapsulatum/1-quality/fastq/SRR949270_2.fastq.unpaired CROP:100 01:40:56 [INFO ] Running step hostAlignment... 01:40:56 [INFO ] ===> cp ../sampleData/hostRef/Homo_sapiens_GRCh38.fna ../hcapsulatum/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa 01:41:31 [INFO ] Building STAR index file for Homo_sapiens_GRCh38... 01:41:31 [INFO ] ===> Job 96561: STAR --runThreadN 16 --runMode genomeGenerate --genomeSAindexNbases 6 --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --genomeFastaFiles ../hcapsulatum/2-alignment/host/genomes/Homo_sapiens_GRCh38/genome.fa --genomeSAsparseD 1 > ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star.done 01:41:31 [INFO ] Mapping SRR950197_1.fastq and SRR950197_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96562: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR950197_1.fastq ../hcapsulatum/1-quality/fastq/SRR950197_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950197 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950197Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR950197_star.sam 01:41:31 [INFO ] Mapping SRR950198_1.fastq and SRR950198_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96563: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR950198_1.fastq ../hcapsulatum/1-quality/fastq/SRR950198_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950198 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950198Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR950198_star.sam 01:41:31 [INFO ] Mapping SRR949916_1.fastq and SRR949916_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96564: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR949916_1.fastq ../hcapsulatum/1-quality/fastq/SRR949916_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949916 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949916Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949916_star.sam 01:41:31 [INFO ] Mapping SRR950093_1.fastq and SRR950093_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96565: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR950093_1.fastq ../hcapsulatum/1-quality/fastq/SRR950093_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950093 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950093Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR950093_star.sam 01:41:31 [INFO ] Mapping SRR949601_1.fastq and SRR949601_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96566: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR949601_1.fastq ../hcapsulatum/1-quality/fastq/SRR949601_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949601 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949601Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949601_star.sam 01:41:31 [INFO ] Mapping SRR949624_1.fastq and SRR949624_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96567: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR949624_1.fastq ../hcapsulatum/1-quality/fastq/SRR949624_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949624 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949624Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949624_star.sam 01:41:31 [INFO ] Mapping SRR949060_1.fastq and SRR949060_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96568: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR949060_1.fastq ../hcapsulatum/1-quality/fastq/SRR949060_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949060 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949060Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949060_star.sam 01:41:31 [INFO ] Mapping SRR949270_1.fastq and SRR949270_2.fastq to the reference file... 01:41:31 [INFO ] ===> Job 96569: STAR --runThreadN 16 --runMode alignReads --readFilesIn ../hcapsulatum/1-quality/fastq/SRR949270_1.fastq ../hcapsulatum/1-quality/fastq/SRR949270_2.fastq --genomeDir ../hcapsulatum/2-alignment/host/indices/Homo_sapiens_GRCh38_star --outFileNamePrefix ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949270 --outSAMunmapped Within --outReadsUnmapped Fastx --limitGenomeGenerateRAM 31000000000 && mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949270Aligned.out.sam ../hcapsulatum/2-alignment/host/sam/Homo_sapiens_GRCh38/SRR949270_star.sam 02:59:19 [INFO ] Running step removeAligned... 02:59:19 [INFO ] ===> Job 96570: 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 02:59:19 [INFO ] ===> Job 96571: 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 02:59:19 [INFO ] ===> Job 96572: 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 02:59:19 [INFO ] ===> Job 96573: 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 02:59:19 [INFO ] ===> Job 96574: 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 02:59:19 [INFO ] ===> Job 96575: 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 02:59:19 [INFO ] ===> Job 96576: 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 02:59:19 [INFO ] ===> Job 96577: 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 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950197Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR950197_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950197Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR950197_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950198Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR950198_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950198Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR950198_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949916Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR949916_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949916Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR949916_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950093Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR950093_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR950093Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR950093_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949601Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR949601_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949601Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR949601_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949624Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR949624_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949624Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR949624_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949060Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR949060_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949060Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR949060_2.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949270Unmapped.out.mate1 ../hcapsulatum/2-alignment/host/fastq/SRR949270_1.fastq 03:02:55 [INFO ] ===> mv ../hcapsulatum/2-alignment/host/star/Homo_sapiens_GRCh38/SRR949270Unmapped.out.mate2 ../hcapsulatum/2-alignment/host/fastq/SRR949270_2.fastq 03:11:24 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR950197.unmapped.fastq 03:19:57 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR950198.unmapped.fastq 03:28:39 [INFO ] ===> rm ../hcapsulatum/2-alignment/host/fastq/SRR949916.unmapped.fastq