Clinker just stalls without producing output?

Hello,

I am running Clinker on a server (installed via conda) for five genomes (from the same genus); gbk files were downloaded from GenBank. I use the following command: clinker ./genomes/*.gbk -p results.html The problem is that after ~2.5 hours, it seems that the procedure stalls without producing any output. I found that during these 2.5 hours, python processes (one per CPU) were active, but then they stopped, and nothing happened after.
When I do not align the clusters (-na option), everything works, and the desired output file is produced (although without cluster alignments, it not useful).

Any ideas what may cause this?

Thank you!

[gamcil]

A while back I added the --ranges argument where you can specify genomic coordinates to be extracted (e.g. --ranges scaffold_1:10000-50000). Though, some people were having issues with it (https://github.com/gamcil/clinker/issues/62) and I haven’t had time to go back and look, so just check if you can get it working. Otherwise, there’s bound to be scripts around to extract regions from GenBank files, or you can do it through graphical software like Geneious.

[hyphaltip]

to extract ranges of genomes this is very easy with biopython eg here’s part of one script that does this https://github.com/stajichlab/GAG_cluster_1kfg/blob/7c14b29bd3a9f1401e0896010930a3f7a5ede5f4/scripts/build_cluster_genbank.py#L155

from Bio import SeqIO
seq = SeqIO.read("GENBANKFILE.gb", "genbank")
left = 100
right = 10000
slice = seq[ left:right ] # cut a slice out
SeqIO.write(slice, "GENBANK_SLICE.gbk", "genbank")