bam option looks for jgi_summarize_bam_contig_depths

[gabriellerocap]

Hi Arkadiy Thanks for your work developing FeGenie. I installed it on a MacBookPro with Conda and the basic commands are working on my dataset, but when I tried to use the -bam option I got the following error.

processing... GeoMICS_all_contigs.fa
sh: jgi_summarize_bam_contig_depths: command not found
processing... GeoMICS_all_contigs.fa
Traceback (most recent call last):
  File "/Users/gabrielle/Desktop/GenomeFun/FeGenie/FeGenie.py", line 2293, in main
    depth = open("%s/contigDepths/%s.depth" % (args.out, cell))
FileNotFoundError: [Errno 2] No such file or directory: 'geomics_all_bam_test_out/contigDepths/GeoMICS_all_contigs.fa.depth'

I recognized this script name from my prior efforts at binning this metagenome, so I just installed metabat2 in the same Conda environment and now the bam option appears to work. I am sure this is not the preferred solution, posting here in case it helps someone else or to get a better fix.

[Arkadiy-Garber]

Hi,

Thanks for letting me know about this issue. FeGenie uses the jgi_summarize_bam_contig_depths from the Metabat package to extract read coverage information from each contig. There might be a better way to do it, but it seemed like the simplest at the time of writing this program. I just added metabat2 to the conda installation script setup.sh, so that it is included in the FeGenie environment. I'll look into getting a better fix soon.

Thanks for using FeGenie! Let me know if you have any other questions or issues. Arkadiy

[gabriellerocap]

Thank you! I deleted my FeGenie conda environment and reinstalled this morning according to your conda instructions and the bam option is working now with no additional tweaks needed.

[Arkadiy-Garber]

Awesome, glad that it works now! Thanks for testing it out and letting me know.

Cheers, Arkadiy