+ SRR=SRR519926
+ N=1000
+ mkdir -p reads
+ mkdir -p reports
+ READ1=reads/SRR519926_1.fastq
+ READ2=reads/SRR519926_2.fastq
+ GOOD1=reads/good1.fq
+ GOOD2=reads/good2.fq
+ BAD1=reads/bad1.fq
+ BAD2=reads/bad2.fq
+ fastq-dump -X 1000 -O reads --split-files SRR519926
+ fastqc reads/SRR519926_1.fastq reads/SRR519926_2.fastq
Started analysis of SRR519926_1.fastq
Approx 100% complete for SRR519926_1.fastq
Started analysis of SRR519926_2.fastq
Approx 100% complete for SRR519926_2.fastq
+ trimmomatic PE reads/SRR519926_1.fastq reads/SRR519926_2.fastq reads/good1.fq reads/bad1.fq reads/good2.fq reads/bad2.fq SLIDINGWINDOW:4:30
TrimmomaticPE: Started with arguments:
 reads/SRR519926_1.fastq reads/SRR519926_2.fastq reads/good1.fq reads/bad1.fq reads/good2.fq reads/bad2.fq SLIDINGWINDOW:4:30
Multiple cores found: Using 4 threads
Quality encoding detected as phred33
Input Read Pairs: 1000 Both Surviving: 749 (74.90%) Forward Only Surviving: 184 (18.40%) Reverse Only Surviving: 18 (1.80%) Dropped: 49 (4.90%)
TrimmomaticPE: Completed successfully
+ fastqc -o reports reads/good1.fq reads/bad1.fq reads/good2.fq reads/bad2.fq
Started analysis of good1.fq
Started analysis of bad1.fq
Started analysis of good2.fq
Started analysis of bad2.fq