Question: Stacks error:failed to gz-open
0
gravatar for mahnazkiani
7 months 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 • 291 views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 7 months ago by mahnazkiani50
1

what is the output of:

find  stacks_out -type f
ADD REPLYlink written 7 months ago by Pierre Lindenbaum126k

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 7 months ago by mahnazkiani50

For future reference, whenever you have an issue running STACKS, you can look for a solution or post your issue in the STACKS google group. Julian Catchen is very good at providing assistance.

ADD REPLYlink written 7 months ago by Giovanni.madrigal12130
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