lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats

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Fail to open input file/stream

XueWang2019 opened this issue · comments

commented

I use SRAtoolkit from NCBI to convert a RUN SAR14514455 to fastq file as below:
image

Then I use seqtk to convert fastq to fasta file with the below command:
image

The new fasta file is created but is empty.
The error info is:
[E::stk_seq] failed to open the input file/stream.

The fastq file is as below:
image

I am a newbie in the bio info area. Could you pls help with it? Thanks.

Please check the input path using ls. And the output path /srrxxx.fasta should be invalid, cause you may have no write permission in the root path /, try

seqtk seq -A /mnt/xxxx.fastq > srxxxx.fasta