rnaquast conda error

[kathrinannaotte]

Hi @rivera10 ,

when runnning the test sample almost the whole pipeline worked for me! However, the very last evaluation step using rnaquast failed with the error message:

`error executing process > 'rna_quast (Sponge_sample)'

Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /home/kathrin/postdoc_vienna/de_novo/test_transpi/work/conda/env-fa8b0a403402a49160ee9bce39b0a3c5 -c conda-forge bioconda::rnaquast=2.0.1=0
status : 143
message:
Might it be a compatibility/dependency issue? When I just run conda create --mkdir --yes --quiet --prefix /home/kathrin/postdoc_vienna/de_novo/test_transpi/work/conda/env-fa8b0a403402a49160ee9bce39b0a3c5 -c conda-forge bioconda::rnaquast=2.0.1=0 I get this outputconda create --mkdir --yes --quiet --prefix /home/kathrin/postdoc_vienna/de_novo/test_transpi/work/conda/env-fa8b0a403402a49160ee9bce39b0a3c5 -c conda-forge bioconda::rnaquast=2.0.1=0
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...`
which runs forever (or at least until I stopped it after several hours).

I installed conda (anaconda3) using your precheck script

All the best
Kathrin

[kathrinannaotte]

Upate: I can run rnaquast when creating a conda environment with gffutils and then installing rnaquast in this environment:

conda create -n test2 --yes -c conda-forge gffutils
conda activate test2
conda install bioconda::rnaquast=2.0.1=0

Resolving the environment still takes approx. 15 minutes, though. Is there anything I can do to make it run in the context of transpi?

Thank you and all the best
Kathrin

[rivera10]

Hello @kathrinannaotte,

Yes, rna-quast sometimes takes a long time in the creation of the env. You could clean all the packages and files (conda clean --all ) before running the pipeline with the resume option.

Also, it could be the version of rna-quast you are using. At the moment TransPi uses rna-quast 2.2.1=h9ee0642_0. I will recommend to pull again the repository. If the issue still continues, you could create the env before the pipeline is executed. For this you will need to have the hash number of the environment. I can provide you with details of this if the issue continues, since it requieres to go to a specific directory and look for some files.

Best,
Ramon

[laninsky]

Hi Ramon and Kathrina,

I'm running into the same problem, and have tried the conda clean --all option. Below is the error:

Error executing process > 'rna_quast (SRR1578145)'

Caused by:
  Failed to create Conda environment
  command: conda create --mkdir --yes --quiet --prefix /scale_wlg_nobackup/filesets/nobackup/uoo00105/transpi_conda/condaEnv/env-475622de9368222cf2e999f59ba55d9f -c conda-forge bioconda::rnaquast=2.2.1=h9ee0642_0
  status : 143
  message:

Would it be possible to get the details on how to create the env before the pipeline is executed?

Thanks,

Alana

[rivera10]

Hello @laninsky,

You can create the env before running the pipeline by using the following:

conda create --mkdir --yes --quiet --prefix /scale_wlg_nobackup/filesets/nobackup/uoo00105/transpi_conda/condaEnv/env-475622de9368222cf2e999f59ba55d9f -c conda-forge bioconda::rnaquast=2.2.1=h9ee0642_0

I think the issue is that it takes too long for the env to be created and Nextflow is stopping the run. I am looking for ways to change this, if possible.

Once created then you ca resume the previous run. Hope that helps.

Best,
Ramón