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c383d893 / AMF-LSU-Database-and-Pipeline2

Updated Database and pipeline for phylogenetic determination of AMF from environmental sequences
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error creating the AMF_pipeline within conda on HPC #6

Open bashir94 opened 3 months ago

bashir94 commented 3 months ago

I would be glad to implement this pipeline to process my AMF LSU sequences from Illumina Miseq using the "AMF pipeline"; however, I have encountered an error while creating the AMF pipeline environment on my university's HPC. I am following the procedures you have highlighted on the "READ_AMF_LSU_ASV_pipelines"

The error is encountered when running the commandline "conda env create -n "amf_pipeline" --file "amf_pipeline_requirements.yml" " , and the eerror messages are:
CondaHTTPError: HTTP 404 NOT FOUND for url https://packages.qiime2.org/qiime2/2024.2/amplicon/released/linux-64/rescript-2024.2.0-py38hbae55e2_0.tar.bz2
Elapsed: 00:00.751045

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 404 NOT FOUND for url https://packages.qiime2.org/qiime2/2024.2/amplicon/released/linux-64/rescript-2024.2.0-py38hbae55e2_0.tar.bz2
Elapsed: 00:00.751045

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

I will be glad if you can guide me on how to resolve this error.

RobJamesRamos commented 2 months ago

Thanks for raising this issue. The page https://packages.qiime2.org/qiime2/2024.2/amplicon/released/linux-64/ still lists rescript-2024.2.0-py38hbae55e2_0.tar.bz2, but indeed the file seems to be missing. Ill dig around some more on Qiime2 site to see if there is a better download link and we will update the pipeline when we get this figured out.

RobJamesRamos commented 2 months ago

One thing to try is bumping the individual package version number in "amf_pipeline_requirements.yml" from - rescript=2024.2.0 to - rescript=2024.2.2. There is at least one download link for that version that is working here. We did not test the pipeline with that specific package version for rescript, but it might be a good temporary solution.

I will try to open an issue up with Qiime2 in the meantime. At some point I will want to bump our base Qiime2 version which would also fix this issue, but I would want to thoroughly test things before making that Qiime2 version bump public.