Bioinformatics Data Analysis

Results generated by running the recipe.

Parameters used during the run:

  • BioProject Number:PRJNA313294
  • Number of runs per project:5
  • Number of reads per run:2000
Output Messages
Messages printed to the standard output stream:
Read 2000 spots for SRR3191544
Written 2000 spots for SRR3191544
Read 2000 spots for SRR3191545
Written 2000 spots for SRR3191545
Read 2000 spots for SRR3191542
Written 2000 spots for SRR3191542
Read 2000 spots for SRR3191543
Written 2000 spots for SRR3191543
Rejected 2000 READS because READLEN < 1
Read 2000 spots for SRR3194428
Written 2000 spots for SRR3194428
Analysis complete for SRR3191542_1.fastq
Analysis complete for SRR3191542_2.fastq
Analysis complete for SRR3191543_1.fastq
Analysis complete for SRR3191543_2.fastq
Analysis complete for SRR3191544_1.fastq
Analysis complete for SRR3191544_2.fastq
Analysis complete for SRR3191545_1.fastq
Analysis complete for SRR3191545_2.fastq
Analysis complete for SRR3194428_1.fastq
Other Messages
Messages printed to the standard error stream:
+ PRJN=PRJNA313294
+ RUNS=5
+ READS=2000
+ esearch -db sra -query PRJNA313294
+ efetch -format runinfo
+ cat runinfo.csv
+ cut -f 1 -d ,
+ head -5
+ grep SRR
+ mkdir -p reads
+ cat runids.txt
+ parallel fastq-dump --split-files -X 2000 -outdir reads '{}'
+ mkdir -p fastqc
+ fastqc -o fastqc reads/SRR3191542_1.fastq reads/SRR3191542_2.fastq reads/SRR3191543_1.fastq reads/SRR3191543_2.fastq reads/SRR3191544_1.fastq reads/SRR3191544_2.fastq reads/SRR3191545_1.fastq reads/SRR3191545_2.fastq reads/SRR3194428_1.fastq
Started analysis of SRR3191542_1.fastq
Approx 50% complete for SRR3191542_1.fastq
Approx 100% complete for SRR3191542_1.fastq
Started analysis of SRR3191542_2.fastq
Approx 50% complete for SRR3191542_2.fastq
Approx 100% complete for SRR3191542_2.fastq
Started analysis of SRR3191543_1.fastq
Approx 50% complete for SRR3191543_1.fastq
Approx 100% complete for SRR3191543_1.fastq
Started analysis of SRR3191543_2.fastq
Approx 50% complete for SRR3191543_2.fastq
Approx 100% complete for SRR3191543_2.fastq
Started analysis of SRR3191544_1.fastq
Approx 45% complete for SRR3191544_1.fastq
Approx 100% complete for SRR3191544_1.fastq
Started analysis of SRR3191544_2.fastq
Approx 50% complete for SRR3191544_2.fastq
Approx 100% complete for SRR3191544_2.fastq
Started analysis of SRR3191545_1.fastq
Approx 45% complete for SRR3191545_1.fastq
Approx 100% complete for SRR3191545_1.fastq
Started analysis of SRR3191545_2.fastq
Approx 50% complete for SRR3191545_2.fastq
Approx 100% complete for SRR3191545_2.fastq
Started analysis of SRR3194428_1.fastq
Approx 45% complete for SRR3194428_1.fastq
Approx 100% complete for SRR3194428_1.fastq
+ rm -f fastqc/ fastqc/ fastqc/ fastqc/ fastqc/ fastqc/ fastqc/ fastqc/ fastqc/

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