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Fastq dump error

Hi I'm getting the following error while converting the sra to fastq using fastq dump:

fastq-dump.2.5.7 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='4'

tried the usual places but not able to find a solution to this.

sratoolkit fastq sra
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updated by Ram Ram • written by aj123 aj123

Looks like you run out of space.

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written by trausch trausch

1 answer

Likely storage issue, also check this out error report：while running fastq-dump

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updated by Ram Ram • written by Sukhi Singh Sukhi Singh

Note also that fastq-dump by default places a cache file in your home directory which it does not remove after completed download. So it might as well be your home partition that is filled up.

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written by Michael Dondrup Michael Dondrup

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