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farhat-lab / gentb-snakemake

From FASTQ file to antibiotic resistance prediction using RandomForest - the GenTB pipeline wrapped in snakemake
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Snakemake Workflow failed #6

Open M-Serajian opened 1 year ago

M-Serajian commented 1 year ago

Hello,

I want to kindly inform you that the dependencies of the Gentb-snakemake are not updated which caused me not to be able to set up the Conda environment. I could solve the issue and install the environment, but still, after running it, I got multiple errors in the pilon rules. I increased both the time and memory for this rule in the cluster.json; nevertheless, this problem still exists and unfortunately deprived us of using it. I have uploaded the .log files for your consideration.

Thanks Best M.S.

gentb_workflow_3392622.log gentb_workflow_3743549.log

mahafarhat commented 11 months ago

Sorry about the delay. Thanks for attaching the log files. We will look into this issue.

doctormo commented 11 months ago

@M-Serajian Do you still have the log file /blue/boucher/m.serajian/Final_TB/Deep_TB/GenTB/gentb-snakemake/.snakemake/log/2023-07-20T114312.454282.snakemake.log and if so, could you upload it here?