Q: Stuck with initialisation of a workflow (atac-seq) about seq2science HOT 13 CLOSED

Thanks for the issue, I'll take a look. Probably after the weekend I have an answer for you

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Could you post what's in this file: /Users/u0107886/Stefanie/results/log/trackhub/ASM14944v2.index.log

On what kind of computer are you running it? Linux, Mac, or Windows?

from seq2science.

ASM14944v2.index.log

Thanks for your very quick response!! We are running it on a Mac, 4 cores. 32gb mom

from seq2science.

I can't reproduce the error, but I think it's because mac has a different version of grep than linux. Could you add grep to the environment that's needed for the trackhub index? That's file:

/Users/u0107886/miniconda/envs/seq2science/lib/python3.8/site-packages/seq2science/rules/../envs/ucsc.yaml, and then add grep so that it looks like this:

name: ucsc
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bioconda::grep=3.4
  - bioconda::ucsc-bedsort=377
  - bioconda::ucsc-bedGraphToBigWig=377
  - bioconda::ucsc-bedToBigBed=377
  - bioconda::ucsc-fatotwobit=377
  - bioconda::ucsc-gtftogenepred=377
  - bioconda::ucsc-genepredtobed=377
  - bioconda::ucsc-hggcpercent=377
  - bioconda::ucsc-ixixx=377
  - bioconda::ucsc-wigtobigwig=377
  - conda-forge::conda-ecosystem-user-package-isolation=1.0

And then run seq2science as you normally would. It should re-install the environment, with GNU grep added, and hopefully this works then 😄!

Let me know if that solves the issue for you. As a last resort solution you can always set create_trackhub: false so that no ucsc trackhub is made which hopefully run the rest of the pipeline successfully

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Hey! Thanks for that! I had to set the create_trackhub to false...
The workflow ran, but got stuck near the end...
I attached the error log.
seq2science.2022-12-22T101835.775224.log

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from seq2science.

Hey!

Thanks already for all your help!
to recap: Trackhub is still set to false,
deeptools_qc is also set to false. it then runs till the error attached below.
I looked for this error in previous issue mentions and found it here
#625

but I don't see what is changed to overcome this issue.

Kind regards,
Wouter
seq2science.2023-01-03T143400.407190.log

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Can you post the log of the actual rule that fails?

/Users/u0107886/Stefanie/results/log/combine_peaks/ASM14944v2-macs2.log

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Next time I'll immediately include that!

ASM14944v2-macs2.log

from seq2science.

That one I actually solved yesterday (I think). At the end of today there will be a new seq2science release. Hopefully everything works for you with that version

from seq2science.

You can try mamba install seq2science=0.9.7 tomorrow in your seq2science environment, and seq2science should be updated to the newest version. Please let me know if it works then 🙏

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The issue you had was with conda and the newest numpy version. I've changed the description on which numpy version should be used on the bioconda side, so probably removing the environment and just restarting the run with the current seq2science version also works btw.

rm -r ../miniconda/envs/seq2science/lib/python3.8/site-packages/seq2science/.snakemake/cd6528626806a6e527f5cf7769376ea3_
seq2science run ...

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I'm assuming this has been resolved, feel free to reopen if not

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