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antonisdim / haystac

Code repository for the HAYSTAC pipeline
MIT License
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Analyse --mode reads error- missing script #3

Closed Pkaps25 closed 3 years ago

Pkaps25 commented 3 years ago

Hello,

I am able to run haystac analyse --mode abundances, but haystac analyse --mode reads fails. I've included the snakemake log. My goal is to recover the reads that are being assigned to each category, i.e. dark and grey matter, but it looks like this code may have been refactored. haystaclog.txt

I installed haystac through conda. Thank you for your help and please let me know if I can provide more information.

Best, Peter

antonisdim commented 3 years ago

Hello Peter,

I hope you are doing great and apologies for not getting back to you earlier !

Thank you for using haystac and for raising this issue.

Indeed the code for haystac analyse --mode reads has been recently refactored and optimised as a new version will be released soon on conda.

I went through the log file and I was wondering if you could upload the likelihood matrix that haystac analyse --mode abundances has produced, as it would helpful to double check that reads have been assigned to the grey matter. From your log file it should be here /local/workdir/pk445/haystac/both_notrim_reads_.05/probabilities/both_sample/both_sample_likelihood_ts_tv_matrix.csv.

I will make sure I get back to you ASAP.

Thank you for your help and patience !

Best, Antony

Pkaps25 commented 3 years ago

Hello Antony,

Thanks for the response. In the meantime, is there a workaround for using this feature?

edit: Solved by using the setup command in the example directory.