Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • SRA Run Number: SRR1972973
Output Messages
Messages printed to the standard output stream:
Read 10000 spots for SRR1972973
Written 10000 spots for SRR1972973
Analysis complete for SRR1972973_1.fastq
Analysis complete for SRR1972973_2.fastq
Analysis complete for SRR1972973.trimmed_1P.fq
Analysis complete for SRR1972973.trimmed_1U.fq
Analysis complete for SRR1972973.trimmed_2P.fq
Analysis complete for SRR1972973.trimmed_2U.fq
Other Messages
Messages printed to the standard error stream:
Started analysis of SRR1972973_1.fastq
Approx 10% complete for SRR1972973_1.fastq
Approx 20% complete for SRR1972973_1.fastq
Approx 30% complete for SRR1972973_1.fastq
Approx 40% complete for SRR1972973_1.fastq
Approx 50% complete for SRR1972973_1.fastq
Approx 60% complete for SRR1972973_1.fastq
Approx 70% complete for SRR1972973_1.fastq
Approx 80% complete for SRR1972973_1.fastq
Approx 90% complete for SRR1972973_1.fastq
Approx 100% complete for SRR1972973_1.fastq
Started analysis of SRR1972973_2.fastq
Approx 10% complete for SRR1972973_2.fastq
Approx 20% complete for SRR1972973_2.fastq
Approx 30% complete for SRR1972973_2.fastq
Approx 40% complete for SRR1972973_2.fastq
Approx 50% complete for SRR1972973_2.fastq
Approx 60% complete for SRR1972973_2.fastq
Approx 70% complete for SRR1972973_2.fastq
Approx 80% complete for SRR1972973_2.fastq
Approx 90% complete for SRR1972973_2.fastq
Approx 100% complete for SRR1972973_2.fastq
TrimmomaticPE: Started with arguments:
 reads/SRR1972973_1.fastq reads/SRR1972973_2.fastq -baseout reads/SRR1972973.trimmed.fq ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20
Multiple cores found: Using 4 threads
Using templated Output files: reads/SRR1972973.trimmed_1P.fq reads/SRR1972973.trimmed_1U.fq reads/SRR1972973.trimmed_2P.fq reads/SRR1972973.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: 4522 (45.22%) Forward Only Surviving: 5362 (53.62%) Reverse Only Surviving: 93 (0.93%) Dropped: 23 (0.23%)
TrimmomaticPE: Completed successfully
Started analysis of SRR1972973.trimmed_1P.fq
Approx 20% complete for SRR1972973.trimmed_1P.fq
Approx 40% complete for SRR1972973.trimmed_1P.fq
Approx 65% complete for SRR1972973.trimmed_1P.fq
Approx 85% complete for SRR1972973.trimmed_1P.fq
Started analysis of SRR1972973.trimmed_1U.fq
Approx 15% complete for SRR1972973.trimmed_1U.fq
Approx 35% complete for SRR1972973.trimmed_1U.fq
Approx 55% complete for SRR1972973.trimmed_1U.fq
Approx 75% complete for SRR1972973.trimmed_1U.fq
Approx 90% complete for SRR1972973.trimmed_1U.fq
Started analysis of SRR1972973.trimmed_2P.fq
Approx 20% complete for SRR1972973.trimmed_2P.fq
Approx 40% complete for SRR1972973.trimmed_2P.fq
Approx 65% complete for SRR1972973.trimmed_2P.fq
Approx 85% complete for SRR1972973.trimmed_2P.fq
Started analysis of SRR1972973.trimmed_2U.fq

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