Running islandpath on fragmented genomes (several contigs)

[HaimAshk]

Hi,

Thanks for maintaining this tool!
Is it possible to use islandpath to search for genomic islands in a somewhat fragmented assembly? It seems only the first LOCUS sequence in the gene-bank file is processed, is that true? Therefor for somewhat fragmented assemblies I find no islands at all, can you please advise?

I also get this warning from the second LOCUS sequence, I tried to fix it in the code but seems fixing it creates another problem downstream.
print() on closed filehandle $PTT_OUT at islandpath_DIMOB_v1.0.6/install/islandpath-1.0.6-conda/lib/GenomeUtils.pm line 471, <GEN1>

Should I split the GeneBank file into separate files, each with a single LOCUS record?

Thanks for any advice,
Haim

[TobiasWinter97]

Have you figure out the resolution? So we should split the GeneBank file into separate files?