+ N=10000 + mkdir -p reads + fastq-dump --split-files -X 10000 -O reads SRR3191542 + mkdir -p reports + fastqc reads/SRR3191542_1.fastq reads/SRR3191542_2.fastq -o reports Started analysis of SRR3191542_1.fastq Approx 10% complete for SRR3191542_1.fastq Approx 20% complete for SRR3191542_1.fastq Approx 25% complete for SRR3191542_1.fastq Approx 40% complete for SRR3191542_1.fastq Approx 45% complete for SRR3191542_1.fastq Approx 60% complete for SRR3191542_1.fastq Approx 65% complete for SRR3191542_1.fastq Approx 80% complete for SRR3191542_1.fastq Approx 90% complete for SRR3191542_1.fastq Approx 100% complete for SRR3191542_1.fastq Started analysis of SRR3191542_2.fastq Approx 10% complete for SRR3191542_2.fastq Approx 20% complete for SRR3191542_2.fastq Approx 25% complete for SRR3191542_2.fastq Approx 40% complete for SRR3191542_2.fastq Approx 45% complete for SRR3191542_2.fastq Approx 60% complete for SRR3191542_2.fastq Approx 65% complete for SRR3191542_2.fastq Approx 80% complete for SRR3191542_2.fastq Approx 90% complete for SRR3191542_2.fastq Approx 100% complete for SRR3191542_2.fastq + echo '>illumina' + echo AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC + trimmomatic PE reads/SRR3191542_1.fastq reads/SRR3191542_2.fastq -baseout reads/SRR3191542.trimmed.fq ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20 TrimmomaticPE: Started with arguments: reads/SRR3191542_1.fastq reads/SRR3191542_2.fastq -baseout reads/SRR3191542.trimmed.fq ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20 Multiple cores found: Using 4 threads Using templated Output files: reads/SRR3191542.trimmed_1P.fq reads/SRR3191542.trimmed_1U.fq reads/SRR3191542.trimmed_2P.fq reads/SRR3191542.trimmed_2U.fq Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 1 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Quality encoding detected as phred33 Input Read Pairs: 10000 Both Surviving: 9469 (94.69%) Forward Only Surviving: 477 (4.77%) Reverse Only Surviving: 26 (0.26%) Dropped: 28 (0.28%) TrimmomaticPE: Completed successfully + fastqc reads/SRR3191542.trimmed_1P.fq reads/SRR3191542.trimmed_1U.fq reads/SRR3191542.trimmed_2P.fq reads/SRR3191542.trimmed_2U.fq -o reports Started analysis of SRR3191542.trimmed_1P.fq Approx 5% complete for SRR3191542.trimmed_1P.fq Approx 20% complete for SRR3191542.trimmed_1P.fq Approx 30% complete for SRR3191542.trimmed_1P.fq Approx 40% complete for SRR3191542.trimmed_1P.fq Approx 50% complete for SRR3191542.trimmed_1P.fq Approx 60% complete for SRR3191542.trimmed_1P.fq Approx 70% complete for SRR3191542.trimmed_1P.fq Approx 80% complete for SRR3191542.trimmed_1P.fq Approx 95% complete for SRR3191542.trimmed_1P.fq Started analysis of SRR3191542.trimmed_1U.fq Started analysis of SRR3191542.trimmed_2P.fq Approx 5% complete for SRR3191542.trimmed_2P.fq Approx 15% complete for SRR3191542.trimmed_2P.fq Approx 30% complete for SRR3191542.trimmed_2P.fq Approx 40% complete for SRR3191542.trimmed_2P.fq Approx 50% complete for SRR3191542.trimmed_2P.fq Approx 60% complete for SRR3191542.trimmed_2P.fq Approx 70% complete for SRR3191542.trimmed_2P.fq Approx 80% complete for SRR3191542.trimmed_2P.fq Approx 95% complete for SRR3191542.trimmed_2P.fq Started analysis of SRR3191542.trimmed_2U.fq + rm -f reports/SRR3191542_1_fastqc.zip reports/SRR3191542_2_fastqc.zip reports/SRR3191542.trimmed_1P_fastqc.zip reports/SRR3191542.trimmed_1U_fastqc.zip reports/SRR3191542.trimmed_2P_fastqc.zip reports/SRR3191542.trimmed_2U_fastqc.zip