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Bioinformatics Data Analysis

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Results for Download sequencing data from an NCBI Bioproject: PRJNA257197, 5, 2000

Results generated by running the recipe.

Completed
• Runtime 37 seconds • updated 5.2 years ago by Istvan Albert
Recipe Code Rerun Recipe Edit Result Delete Result

Results generated by running the recipe.

Parameters used during the run:

  • BioProject Number:PRJNA257197
  • 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 SRR1972921
Written 2000 spots for SRR1972921
Read 2000 spots for SRR1972917
Written 2000 spots for SRR1972917
Read 2000 spots for SRR1972920
Written 2000 spots for SRR1972920
Read 2000 spots for SRR1972919
Written 2000 spots for SRR1972919
Read 2000 spots for SRR1972918
Written 2000 spots for SRR1972918
Analysis complete for SRR1972917_1.fastq
Analysis complete for SRR1972917_2.fastq
Analysis complete for SRR1972918_1.fastq
Analysis complete for SRR1972918_2.fastq
Analysis complete for SRR1972919_1.fastq
Analysis complete for SRR1972919_2.fastq
Analysis complete for SRR1972920_1.fastq
Analysis complete for SRR1972920_2.fastq
Analysis complete for SRR1972921_1.fastq
Analysis complete for SRR1972921_2.fastq
Other Messages
Messages printed to the standard error stream:
+ PRJN=PRJNA257197
+ RUNS=5
+ READS=2000
+ esearch -db sra -query PRJNA257197
+ efetch -format runinfo
+ cat runinfo.csv
+ grep SRR
+ head -5
+ cut -f 1 -d ,
+ mkdir -p reads
+ cat runids.txt
+ parallel fastq-dump --split-files -X 2000 -outdir reads '{}'
+ mkdir -p fastqc
+ fastqc -o fastqc reads/SRR1972917_1.fastq reads/SRR1972917_2.fastq reads/SRR1972918_1.fastq reads/SRR1972918_2.fastq reads/SRR1972919_1.fastq reads/SRR1972919_2.fastq reads/SRR1972920_1.fastq reads/SRR1972920_2.fastq reads/SRR1972921_1.fastq reads/SRR1972921_2.fastq
Started analysis of SRR1972917_1.fastq
Approx 50% complete for SRR1972917_1.fastq
Approx 100% complete for SRR1972917_1.fastq
Started analysis of SRR1972917_2.fastq
Approx 50% complete for SRR1972917_2.fastq
Approx 100% complete for SRR1972917_2.fastq
Started analysis of SRR1972918_1.fastq
Approx 50% complete for SRR1972918_1.fastq
Approx 100% complete for SRR1972918_1.fastq
Started analysis of SRR1972918_2.fastq
Approx 50% complete for SRR1972918_2.fastq
Approx 100% complete for SRR1972918_2.fastq
Started analysis of SRR1972919_1.fastq
Approx 50% complete for SRR1972919_1.fastq
Approx 100% complete for SRR1972919_1.fastq
Started analysis of SRR1972919_2.fastq
Approx 50% complete for SRR1972919_2.fastq
Approx 100% complete for SRR1972919_2.fastq
Started analysis of SRR1972920_1.fastq
Approx 50% complete for SRR1972920_1.fastq
Approx 100% complete for SRR1972920_1.fastq
Started analysis of SRR1972920_2.fastq
Approx 50% complete for SRR1972920_2.fastq
Approx 100% complete for SRR1972920_2.fastq
Started analysis of SRR1972921_1.fastq
Approx 50% complete for SRR1972921_1.fastq
Approx 100% complete for SRR1972921_1.fastq
Started analysis of SRR1972921_2.fastq
Approx 50% complete for SRR1972921_2.fastq
Approx 100% complete for SRR1972921_2.fastq
+ rm -f fastqc/SRR1972917_1_fastqc.zip fastqc/SRR1972917_2_fastqc.zip fastqc/SRR1972918_1_fastqc.zip fastqc/SRR1972918_2_fastqc.zip fastqc/SRR1972919_1_fastqc.zip fastqc/SRR1972919_2_fastqc.zip fastqc/SRR1972920_1_fastqc.zip fastqc/SRR1972920_2_fastqc.zip fastqc/SRR1972921_1_fastqc.zip fastqc/SRR1972921_2_fastqc.zip

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