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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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Fail to open input file/stream #186

Open XueWang2019 opened 2 years ago

XueWang2019 commented 2 years ago

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.

shenwei356 commented 2 years ago

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