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Nextflow version 23.10.0 is incompatible with QIIME2 (pipeline fails), solution: prepend 'NXF_VER=23.04.4' when running the pipeline #654
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Thanks for the report!
Conclusion: Edit: The error I encountered was related to Process |
Yeap, that worked. Thanks! |
Nextflow 23.10 adds the |
Hm quite possible. How to test that?
Correct? |
That is exactly what the error message states, no?
In previous versions, |
I just wanted to confirm the problem on my laptop (to later run with docker; I have installed singularity & docker) with So I tried all 3 systems that I have available at the moment: Failing system (Workstation)
Succeeding system (Laptop):
Succeeding system (hpc):
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Great. In that case, I would imagine two workarounds:
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Thanks @muffato & @MatthiasZepper for your intrest and suggestions! Here is the complete error message for
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I think
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Great, thanks, that did work indeed! |
I checked for examples in pipelines and nf-core/modules and found only very few examples: nf-core/modules: nf-core/marsseq: nf-core/rnafusion So nf-core modules seem to put tmp and home into the work dir Not sure what to conclude here, so different solutions :) |
Another example for your list, @d4straub : In your case, and I know nothing about the tool so I'm just guessing, if it's a "cache", then presumably the tool will not clean it up at the end, since the purpose of a cache is to keep files around for the next run. Using So either consider it a purely temporary necessity and use |
Thanks for that great explanation! I'll test I researched where the older export code is coming from in ampliseq and I found the addition of it in #163. In that PR was a change from |
I think the nf-core #modules channel would be the appropriate place to get some more input on the issue. I am certainly not an expert in this matter, but @muffato 's explanation strikes me as strange. The reason why you do not find many modules or pipelines with explicit configuration is, that many tools just use In summary, I advocate using |
Thanks a lot for your input! |
Fair comment @MatthiasZepper . You're absolutely right regarding what is best practice on a HPC and what you're describing is exactly how things work on ours. One of the problems we're seeing is that tmpwatch is not running soon enough and we're often running out of space on I was recently wondering if I could force something like Coming back to the original error, we're looking for a place to let the tool record some cache files that it won't delete at the end. My view is still that either it is treated as a proper cache and is made a proper Nextflow parameter that the user can select, will be staged, and can be reused between processes / runs. Or, consider it like temporary files that can be trashed after the run. In the latter case, I wouldn't support making it use |
Thanks to all of you here, the fix is in dev branch now, will be in the next release. I close here but feel free to open another issue if you encounter any other problems. |
Description of the bug
FYI, ASV_seqs.fasta is present in the work directory (b12ddbfb05b35bef6eb415cb9f1ef0). I've no clue on the origin of the error.
Command used and terminal output
$ nextflow run nf-core/ampliseq -r '2.7.0' -profile singularity --input ' /mnt/DATA/bioinfo/projects/AmpliseqDir/sampleSheet_16S.tsv' --FW_primer 'CCTACGGGNGGCWGCAG' --RV_primer 'GACTACHVGGGTATCTAATCC' --metadata ' /mnt/DATA/bioinfo/projects/AmpliseqDir/metadata.tsv' --outdir ampliseq_results_16S_2.7.0 --max_cpus 4 --max_memory 15GB
Relevant files
No response
System information
Nextflow version: 23.10.0 build 5889
Hardware: Desktop
Executor: local
Container engine: Singularity
OS: Linux
Version of nf-core/ampliseq: 2.7.0
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