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metaGmetapop / metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
MIT License
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depth_by_pos.tsv is empty #1

Open RyanCook94 opened 3 years ago

RyanCook94 commented 3 years ago

Hello!

I've been trying to run Metapop on four bam files against an assembly of multiple contigs. I've used default parameters and have specified the absolute path to the bam folder, assembly and normalisation file.

As far as I can tell, it loads all of the libraries correctly and the samtools calmd step works. But then I get this error...

[bam_fillmd1] different NM for read 'A00291:127:H5HJKDSXX:1:1556:12879:34976 2:N:0:TCCTGAGC+ACTGCATA': 5 -> 106 Error in { : task 1 failed - "File is empty: metapop_depth_by_pos/PHI73_sorted.depth_by_pos.tsv" Calls: metapop_preprocess -> %dopar% -> Execution halted

In the metapop_temp directory, there are "ANI_filt.bam" and "ANI_filt.bam.bai" for each read library. But all of the "depth_by_pos.tsv" files in the metapop_depth_by_pos directory are empty.

Any ideas what could be causing this?

Please let me know if I've missed anything important (am new to Github!).

metaGmetapop commented 3 years ago

Sorry for the delay in response. We are working on updating the code with python in the front end. We are working on releasing the new version. These errors should be fixed in the newest version. More to come soon.