linearham processing failure -- need help interpreting/solving error message about linearham HOT 4 CLOSED

I should note that I'm trying to run multiple sessions of linearham in the same singularity instance in parallel -- perhaps there is a shared file.

from linearham.

@wfs-lilly sorry for all the roadblocks. This actually seems to be due to some bad assumptions made in the linearham code about partis cluster indices. We are working on it now and will push a fix for --cluster-ind as soon as possible. Thanks for your patience!

from linearham.

@wfs-lilly this should be fixed in #59, which also introduced some changes to how you should specify your cluster of interest - documented here.

Importantly, --cluster-ind as you specified it before will no longer correspond the same cluster with the new --cluster-index option, as the cluster index is now the index of the cluster in a given partition (see documentation linked above for more on this).

To list the clusters in the best partition from partis, run:

scripts/parse_cluster.py \ 
               partition.yaml \
               --fasta-output-file parsed_cluster.fa \
               --yaml-output-file parsed_cluster.yaml

on your partis output file.

Let me know if you have any questions about how this applies to your case. Hope this helps!

from linearham.

@wfs-lilly closing but feel free to re-open if you are still having any issues related to the cluster index not solved by the changed introduced by #59. Thanks!

from linearham.