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EBI-Metagenomics / mobilome-annotation-pipeline

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Python3 incompatibility #36

Closed boykebunk closed 9 hours ago

boykebunk commented 3 weeks ago

While running process > RENAME (1)
an error comes up regarding the python env: Command error: /usr/bin/env: ‘python’: No such file or directory

Most presumably the pipeline is dependent on the servers python environment although not mentioned in the dependencies list. In our case we have installed python3 on the servers, which is not recognized by /usr/bin/env python, but by /usr/bin/env python3, which now should be standard on every new system.

I would recommend to run python2 scripts (if absolutely needed) within a singularity container or to convert them to python3.

mberacochea commented 3 weeks ago

Hi @boykebunk,

All the tools, or at least the majority of them, have a corresponding container. The RENAME process uses a container with Biopython.

Additionally, all the scripts use Python 3, as Python 2 has long been deprecated. Most modern systems have Python 3 as the default Python installation.

Cheers

boykebunk commented 3 weeks ago

Hi @mberacochea ok, good to hear. Then I am still wondering why the error occurs. May I attach the nextflow.log? .nextflow.log

mberacochea commented 3 weeks ago

You should use the singularity profile. I'll amend the documentation (but it's mentioned in the setup instructions), as it's lacking that in the nextflow run examples.

In your case it should be:

$ nextflow run /home/bob10/mobilome-annotation-pipeline/main.nf \
--assembly HEG6_1234.contigs_plasmids.fasta \
-profile singularity

ICEfinder container needs to be built by the users, as per the LICENSE we can't distribute it with the pipeline.

Let me know if you bump into more issues with the pipeline.

boykebunk commented 10 hours ago

Hi @mberacochea after having successfully build the ICE finder container I tried to run again the pipeline. I used: nextflow run /home/bob10/mobilome-annotation-pipeline/main.nf --assembly SWE2_1234.contigs_plasmids.fasta --icefinder_sif /home/bob10/mobilome-annotation-pipeline/templates/icefinder-v1.0-local.sif -profile singularity does not work for me, probably I did not find the correct section within the instructions to build. I am attaching the .nextflow.log again.

mberacochea commented 9 hours ago

I'm moving this to Issue #37