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markowetzlab / scDNAseq-workflow

calling absolute copy numbers on single cell DNA sequencing data - stagging repo for public release
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MissingOutputException in rule scale_scAbsolute #24

Closed annahyan closed 7 months ago

annahyan commented 7 months ago

Hi,

I have a few hundred cells and when I run the pipeline for all, it only completes for a handful and for all the others it throws an error like this:

MissingOutputException in rule scale_scAbsolute in file /path/to/scDNAseq-workflow/workflow/rules/scale_scAbsolute.smk, line 1: Job 142 completed successfully, but some output files are missing. Missing files after 300 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: results/500/smp/smp_cellX.rds

I have already increased the latency time quite a bit (initially it was suggesting to set to 15), but it didn't solve the problem.

Could you please help me with this?

Thanks

leachim commented 7 months ago

Can you identify some of the files that fail? For example, just run it for a subset of cells until you have one or two example cells where it fails. Have you made sure to read all the info in the FAQ and made sure that your input conforms to our requirements? Have you tested the pipeline on our example cells? Snakemake will usually create log files that document the errors for the commands. I would need one of those to help you. This is just a very generic error message.

annahyan commented 7 months ago

Filtering out the cells with low coverage fixed the issue! thanks!