Corona Virus Genome Analysis
All Projects
Run Parameters
Parameters used during the run:
  • The BioProject Number: PRJNA601630

Result description.

Output Messages
Messages printed to the standard output stream:
file                             format  type  num_seqs      sum_len  min_len  avg_len  max_len
/export/sra/SRR10902284_1.fastq  FASTQ   DNA    261,890   90,569,410       80    345.8    3,227
/export/sra/SRR10948550_1.fastq  FASTQ   DNA    425,717  146,271,136       80    343.6    3,227
/export/sra/SRR10948474_1.fastq  FASTQ   DNA    505,484  284,575,255       88      563    8,584
Other Messages
Messages printed to the standard error stream:
+ PRJN=PRJNA601630
+ esearch -db sra -query PRJNA601630
+ efetch -format runinfo
+ cat runinfo.csv
+ cut -f 1 -d ,
+ grep SRR
+ SRA=/export/sra
+ mkdir -p /export/sra
+ cat ids
+ parallel fastq-dump --split-files --outdir /export/sra '{}'
+ mkdir -p fastqc
+ cat ids
+ parallel fastqc -q -o fastqc '/export/sra/{}_1.fastq'
+ cat ids
+ parallel -X -j 1 seqkit stats '/export/sra/{}_1.fastq'

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