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Pore-C-Snakemake test run #53

Closed molecule53 closed 1 year ago

molecule53 commented 1 year ago

Hi,

I am trying out Pore-C-Snakemake with the test data. I am running it on Amazon Elastic Compute Cloud. It has been running for about 24 hrs and remains on "Creating conda environment envs/cooler.yml...Downloading and installing remote packages."

(pore-c-snakemake) ubuntu@ip-172-31-25-247:/Data1/Pore-C-Snakemake$ snakemake --use-conda test -j 4 --config=output_dir=results.test Building DAG of jobs... Creating conda environment envs/pore_c.yml... Downloading and installing remote packages. Environment for envs/pore_c.yml created (location: .snakemake/conda/227bd01d) Creating conda environment envs/cooler.yml... Downloading and installing remote packages.

Screen Shot 2023-03-23 at 10 27 01 AM Screen Shot 2023-03-23 at 10 27 58 AM
eharr commented 1 year ago

This pipeline has been deprecated - please use the new one at: https://github.com/epi2me-labs/wf-pore-c

molecule53 commented 1 year ago

Hello,

Is there a test run I can do first? I tried:

(base) @.***:~$ ./nextflow run epi2me-labs/wf-porec --ubam test_data/porec_test.concatemers.bam --ref test_data/porec_test.genome.fasta --mcool_resolutions 10,20,30

N E X T F L O W ~ version 22.10.7

Pulling epi2me-labs/wf-porec ...

WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-porec/contents/nextflow.config

Remote resource not found: https://api.github.com/repos/epi2me-labs/wf-porec/contents/main.nf

(base) @.***:~$ ls

miniconda3 nextflow output screenlog.0 snap work

Best, Anastasia

From: Eoghan Harrington @.> Sent: Thursday, March 23, 2023 11:03 AM To: nanoporetech/Pore-C-Snakemake @.> Cc: McKinlay, Anastasia @.>; Author @.> Subject: [External] Re: [nanoporetech/Pore-C-Snakemake] Pore-C-Snakemake test run (Issue #53)

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This pipeline has been deprecated - please use the new one at: https://github.com/epi2me-labs/wf-pore-c

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eharr commented 1 year ago

Can you please open an issue on the other repo - they'll be able to support you better.