+ N=10000 + mkdir -p reads + fastq-dump --split-files -X 10000 -O reads SRR519926 + mkdir -p reports + fastqc reads/SRR519926_1.fastq reads/SRR519926_2.fastq -o reports Started analysis of SRR519926_1.fastq Approx 5% complete for SRR519926_1.fastq Approx 20% complete for SRR519926_1.fastq Approx 30% complete for SRR519926_1.fastq Approx 35% complete for SRR519926_1.fastq Approx 50% complete for SRR519926_1.fastq Approx 60% complete for SRR519926_1.fastq Approx 70% complete for SRR519926_1.fastq Approx 80% complete for SRR519926_1.fastq Approx 90% complete for SRR519926_1.fastq Approx 100% complete for SRR519926_1.fastq Started analysis of SRR519926_2.fastq Approx 5% complete for SRR519926_2.fastq Approx 20% complete for SRR519926_2.fastq Approx 30% complete for SRR519926_2.fastq Approx 35% complete for SRR519926_2.fastq Approx 50% complete for SRR519926_2.fastq Approx 60% complete for SRR519926_2.fastq Approx 70% complete for SRR519926_2.fastq Approx 80% complete for SRR519926_2.fastq Approx 90% complete for SRR519926_2.fastq Approx 100% complete for SRR519926_2.fastq + echo '>illumina' + echo AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC + trimmomatic PE reads/SRR519926_1.fastq reads/SRR519926_2.fastq -baseout reads/SRR519926.trimmed.fq ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20 TrimmomaticPE: Started with arguments: reads/SRR519926_1.fastq reads/SRR519926_2.fastq -baseout reads/SRR519926.trimmed.fq ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20 Multiple cores found: Using 4 threads Using templated Output files: reads/SRR519926.trimmed_1P.fq reads/SRR519926.trimmed_1U.fq reads/SRR519926.trimmed_2P.fq reads/SRR519926.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: 8963 (89.63%) Forward Only Surviving: 886 (8.86%) Reverse Only Surviving: 87 (0.87%) Dropped: 64 (0.64%) TrimmomaticPE: Completed successfully + fastqc reads/SRR519926.trimmed_1P.fq reads/SRR519926.trimmed_1U.fq reads/SRR519926.trimmed_2P.fq reads/SRR519926.trimmed_2U.fq -o reports Started analysis of SRR519926.trimmed_1P.fq Approx 10% complete for SRR519926.trimmed_1P.fq Approx 20% complete for SRR519926.trimmed_1P.fq Approx 30% complete for SRR519926.trimmed_1P.fq Approx 40% complete for SRR519926.trimmed_1P.fq Approx 55% complete for SRR519926.trimmed_1P.fq Approx 65% complete for SRR519926.trimmed_1P.fq Approx 75% complete for SRR519926.trimmed_1P.fq Approx 85% complete for SRR519926.trimmed_1P.fq Started analysis of SRR519926.trimmed_1U.fq Started analysis of SRR519926.trimmed_2P.fq Approx 10% complete for SRR519926.trimmed_2P.fq Approx 20% complete for SRR519926.trimmed_2P.fq Approx 30% complete for SRR519926.trimmed_2P.fq Approx 40% complete for SRR519926.trimmed_2P.fq Approx 55% complete for SRR519926.trimmed_2P.fq Approx 65% complete for SRR519926.trimmed_2P.fq Approx 75% complete for SRR519926.trimmed_2P.fq Approx 85% complete for SRR519926.trimmed_2P.fq Started analysis of SRR519926.trimmed_2U.fq + rm -f reports/SRR519926_1_fastqc.zip reports/SRR519926_2_fastqc.zip reports/SRR519926.trimmed_1P_fastqc.zip reports/SRR519926.trimmed_1U_fastqc.zip reports/SRR519926.trimmed_2P_fastqc.zip reports/SRR519926.trimmed_2U_fastqc.zip