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Fastq-dump warning: too many reads at spot id

I want to download a dataset PRJNA281410 from SRA and corresponding reference genome (fasta format) . My code

esearch -db sra -query PRJNA281410 \
| elink -target assembly \
| efetch -format docsum \
| xtract -pattern DocumentSummary -element FtpPath GenBank \
| cut -d ',' -f 1 \
| grep SRR \
| xargs -n 1 -P 4 fastq-dump --split-files --gzip --skip-technical SRR18781516

Warning of skipped lines (many lines of the following warning): fastq-dump warn: too many reads at spot id XXX, maximum YY supported, skipped

References:

fastq-dump
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updated by Pappu Pappu • written by melissachua90 • melissachua90

If you are using xargs to pass values why do you have a fixed SRR18781516 at the end of your command? Additionally your command as posted does not work past the first search step. Many of these datasets are PacBio so I don't think that blanket fastq-dump command will work.

Finally not sure what you mean by

corresponding reference genome (fasta format)

Are you looking to get the reference genomes for the two bacteria that are part of the data?

• 0 views • link
written by GenoMax GenoMax

fastq-dump threw an error without specifying the SRR

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written by melissachua90 • melissachua90

You can check out ENA which also provides fastq files.

• 0 views • link
written by Pappu Pappu

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