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Error with Singularity #427
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Hi Natasha! thanks for opening the issue and letting us know about this problem. The cache shouldn't be removed after every run, that should be just fine. Can you elaborate on which singularity version you are using as well? The error seems indeed a bit odd to me, might need to think a bit more. @nf-core/core anyone else has an idea? |
Hi @apeltzer , Thank you for your reply! We are using Singularity 3.5.3 on EL6. I do agree that the error seems odd - especially that it doesn't happen every time. This is more detailed log from the latest run:
I switched to using conda as a profile, and multiple runs of the same data worked fine. While using conda is a feasible and working solution for me, I am really curious to understand the reason behind the Singularity issue I encountered. Thank you, |
Thank you Natasha for providing more feedback on this! Could you maybe test if its e.g. always failing on the same node? We have a Simply use your command and add
I'd also be interested in finding out what caused this - glad you shared your experience here. |
I did a little bit more searching, and I found this apptainer/singularity#3249 (comment). @apeltzer , I really appreciate you looking into this error with me, and please feel free to close this issue. Thank you, |
Thank you (!) for pointing us towards this issue & thereby resolving another issue we never got fixed (and we know now why!) 🥇 Thank you! Alex |
(I've linked from the other issue to this thread ... -> thanks for that super helpful link to Singularity :-)) |
Hah, I was not aware of the other issue, but I am glad that all unintentionally worked out :) |
Hi,
I was wondering if anyone has encountered the error
Command error: FATAL: resolved path $WORK/.singularity/nfcore-rnaseq-1.4.2.img doesn't match with opened path $WORK/.singularity/nfcore-rnaseq-1.4.2.img (deleted)
when running "rnaseq" with Singularity on a cluster?I don't get this error every time though, just sometimes (usually the second time I run the command), and I haven't been able to figure out what is the reason for that.
The image exists in $WORK/.singularity when I see the error.
I use the following modules and variables:
and the commands I have tried are:
and
Both of them worked the first time, and usually give the error the second time they are executed (not resumed).
Is this a caching issue, and should I remove the cache after every run, or I am missing some additional configuration?
Any suggestions and possible ideas are highly appreciated!
Thank you,
Natasha
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