Ustacks error: Failed to gz.open file

[Mahnaz Kiani]

 

  Hello,

 I am running ustackscommand on stacks v 2.3and geting 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 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

Appriciateyour help.

Mahnaz

[Tiamiyu Bashir]

Hi  Mahnaz, 

How do you manage to solve this error? I'm also faced with this kind of error.

Thank you. 

[flo...@hotmail.fr]

Have you created the folder "stacks_out" ? 
Stacks doesn't create it, it have to exist

If not, you can create it using:

 mkdir stacks_out

Hope that it helps

Florent

[Tiamiyu Bashir]

Thanks Mahnaz, 

I created the output file and it was fixed.

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University of Ilorin,

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[Gracy Buckholtz]

Hi Tiamiyu, 

Were there any files in your output folder? I am getting the same error message but I have no files in the output folder. I am wondering if it is an issue that I have no files ending in .tags.tsv.gz in my output folder since the error says it cannot open file '/ustack_ouput/B46-S_2.1.tags.tsv.gz'. 

Thanks for any help you can provide.  

[Tiamiyu Bashir]

Hi Gracy,

I couldn't solve this, I switched to the denovo approach and everything went well.

Cheers!

Bashir

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[Kaylee Herzog]

Hello Gracy,

I am curious if you found a solution to this issue? I have been struggling with the same error, and similarly have an empty output folder (despite creating in before running ustacks). I appreciate your time.

Cheers,

Kaylee

[Julian Catchen]

Hi Kaylee,

This is some fundamental error that should not happen, that is,
something is wrong on your system, like your disk is full, or you are
running out of memory, something funky is happening with your zlib (for
gzip writing), or similar. This is not likely an issue with Stacks
itself. However, we can't help further without knowing the command you
ran, the Stacks version and outputs from the program, the type of data,
etc.

Best,

julian

Kaylee Herzog wrote on 7/13/21 8:35 AM:

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>
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> *Tiamiyu B. Bashir*
>
> /Department of Plant Biology,/
> /Faculty of Life Sciences,
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Julian M Catchen, Ph.D.
Assistant Professor
Department of Evolution, Ecology, and Behavior
Carl R. Woese Institute for Genomic Biology
University of Illinois, Urbana-Champaign
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[Gracy Buckholtz]

Hi Kaylee, 

Julian is right, it would be helpful to know what kind of data you are working with and what code you ran. I was working with ddRAD-seq data and trying to run the ustacks program. I ended up following Bashir's advice and running the de novo map pipeline which includes the ustacks program and I was able to produce the files I needed. A word of warning: I was working through a compute canada account and the job took around 8 days to run. It might just be that I had a lot of short reads to assemble but if you are going to end up submitting the de novo map job give yourself a lot of time. 

Best! 

Gracy 

[Kaylee Herzog]

Hi all,

@Gracy: Thank you for sharing your experience and advice. I have previously run multiple iterations of the de novo wrapper pipeline as part of my parameter testing, and agree that it can definitely take a good amount of time (even in a remote computing environment) depending on the parameter settings!

@Julian: Thank you for your reply. I am working with SE RAD data in STACKS v. 2.41, 2.53, and 2.55. I encountered the issue in two separate remote computing cluster environments, as well as in a cluster conda environment, in all three STACKS versions, and ruled out RAM and space limits as the cause. Following your response, excellent advice from a colleague, and some additional troubleshooting, I was able to run ustacks successfully in those environments on a single sample using a hard-coded script, and thus determined the issue to result from the formatting of my arrayed submission script. I am now working on reformatting, and anticipate this will solve the issue.

Thanks to you both for your time and your help; they are sincerely appreciated.

Cheers,

Kaylee