Bioinformatics Data Analysis

Results generated by running the recipe.

Parameters used during the run:

  • SRA Run Number:SRR519926
Output Messages
Messages printed to the standard output stream:
Read 10000 spots for SRR519926
Written 10000 spots for SRR519926
Analysis complete for SRR519926_1.fastq
Analysis complete for SRR519926_2.fastq
Analysis complete for SRR519926.trimmed_1P.fq
Analysis complete for SRR519926.trimmed_1U.fq
Analysis complete for SRR519926.trimmed_2P.fq
Analysis complete for SRR519926.trimmed_2U.fq
Other Messages
Messages printed to the standard error stream:
+ 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'
+ 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
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/ reports/ reports/ reports/ reports/ reports/

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