Question: Stacks error:failed to gz-open
0
gravatar for mahnazkiani
16 days ago by
mahnazkiani50
United States
mahnazkiani50 wrote:

Hello,

I am running stacks command on stacks v 2.3and getting following error

"Refetching read IDs...Error: Failed to gz-open file 'stacks_out/DA1_S7_L002_R1_001.1.tags.tsv.gz'. Aborted.

Because I am new on Stacks, I am testing to run a few samples and the code that used was as follows:

ustacks -f DA1_S7_L002_R1_001.1.fq.gz -i 7 -o stacks_out -M 3 -m 3 -p 1

Appreciate your help.

Mahnaz

snp • 106 views
ADD COMMENTlink written 16 days ago by mahnazkiani50
1

what is the output of:

find  stacks_out -type f
ADD REPLYlink written 16 days ago by Pierre Lindenbaum121k

Thank you Pierre, with your hint, I found my mistake by running the command in stacks_out directory and also putting stacks_out as the output directory, I created new directory for output and it solved the issue.

Thanks, Mahnaz

ADD REPLYlink written 16 days ago by mahnazkiani50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1914 users visited in the last hour