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JihedC / Snakemake_ATAC_2020

Repository for Jianhui's snakemake pipeline
MIT License
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Pipeline not working on dev branch #11

Open JihedC opened 3 years ago

JihedC commented 3 years ago

Hi Jianhui,

I was trying to run the pipeline on shark but I have got this error message: ''' Start time : Wed Mar 17 14:35:21 CET 2021 /exports/humgen/jihed/miniconda3/lib/python3.6/site-packages/snakemake/workflow.py:26: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. from snakemake.parser import parse Building DAG of jobs... Creating conda environment envs/homer.yaml... Downloading remote packages. CreateCondaEnvironmentException: Could not create conda environment from /exports/humgen/jihed/Jianhui/Snakemake_ATAC_2020/ATAC-seq_pipeline/rules/../envs/homer.yaml: Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed

ResolvePackageNotFound:

End time : Wed Mar 17 14:35:39 CET 2021 '''

I think there is a mistake with the version of hmmratac. On conda I can find only hmmratac 1.2.10.

Can you fix this please?

WJH58 commented 3 years ago

@JihedC Isn't there problem with homer? Not hmmratac.

JihedC commented 3 years ago

the homer environment contain hmmratac for some reasons. https://github.com/JihedC/Snakemake_ATAC_2020/blob/dev/ATAC-seq_pipeline/envs/homer.yaml

WJH58 commented 3 years ago

@JihedC Since we wrote homer documentation so I deleted homer.yaml and homer.smk. There should be no problem now.

JihedC commented 3 years ago

Ok I'll test it again this week

JihedC commented 3 years ago

The pipeline works on the dev branch, there are some issues with the peak calling but I think it's because the bam files are too small in the test datasets.

WJH58 commented 3 years ago

@JihedC Yes exactly. Test bam files are not paired.

JihedC commented 3 years ago

sorry I meant peak calling with MACS2. And I thought you changed the mapping parameters now to only keep the paired files?

WJH58 commented 3 years ago

@JihedC Yes I have changed the mapping rule and it will produce 100% paired reads.

JihedC commented 3 years ago

Then why do you say that the test bam files are not paired ?