Fail to open input file/stream
XueWang2019 opened this issue · comments
XW commented
I use SRAtoolkit from NCBI to convert a RUN SAR14514455 to fastq file as below:
Then I use seqtk to convert fastq to fasta file with the below command:
The new fasta file is created but is empty.
The error info is:
[E::stk_seq] failed to open the input file/stream.
I am a newbie in the bio info area. Could you pls help with it? Thanks.
Wei Shen commented
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