I am running into a few errors when trying to run islandpath on my own genbank files, but it worked on the example file. The files I'm working with are genbank files produced by prokka (which I think restricted to be single contigs by separating sections containing "//"). The errors I'm getting are similar to https://github.com/brinkmanlab/islandpath/issues/16 abd https://github.com/brinkmanlab/islandpath/issues/14, but I think those both were related to the genbank files containing multiple contigs.
You can see the code I'm using below, and I will attach the input genbank file I'm testing it out with.
singularity exec /home/gdouglas/local/singularity_containers/islandpath.sif islandpath ./Taxa_98.13.gbk test
(Again - the same command with ./NC_003210.gbk specified instead worked fine)
Is there something about the genbank format that I should be looking into? I think perhaps the ptt file is not being created properly, but I'm having a little trouble digging into that as I'm a singularity/docker novice.
This is the error/log output:
Smartmatch is experimental at /usr/local/opt/islandpath/lib/GenomeUtils.pm line 674.
Smartmatch is experimental at /usr/local/opt/islandpath/lib/GenomeUtils.pm line 677.
Smartmatch is experimental at /usr/local/opt/islandpath/lib/GenomeUtils.pm line 852.
/usr/local/opt/islandpath/logger.conf2022/07/22 16:22:38 [main] Logging initialized
2022/07/22 16:22:38 [main] Creating temp directory with needed files
2022/07/22 16:22:38 [main] This is the /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13
2022/07/22 16:22:38 [GenomeUtils] From filename /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13.gbk got /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13, gbk
2022/07/22 16:22:38 [GenomeUtils] Reading genbank format file
2022/07/22 16:22:38 [GenomeUtils] The genome sequence in /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13.gbk has been read.
2022/07/22 16:22:38 [GenomeUtils] Checking contig unknown
2022/07/22 16:22:38 [GenomeUtils] Found sequence in the genbank/embl file
2022/07/22 16:22:38 [GenomeUtils] We have 1 contigs
2022/07/22 16:22:38 [GenomeUtils] From filename /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13.gbk got /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13, gbk
2022/07/22 16:22:38 [GenomeUtils] No base filename given in args, trying to use object default: /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13
2022/07/22 16:22:38 [GenomeUtils] Found formats:
2022/07/22 16:22:38 [GenomeUtils] The genome sequence in /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13.gbk has been read.
2022/07/22 16:22:38 [GenomeUtils] Now generating required file formats (faa, ffn and ptt)
2022/07/22 16:22:38 [GenomeUtils] No base filename given in args, trying to use object default: /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13
2022/07/22 16:22:38 [main] Running IslandPath-DIMOB
2022/07/22 16:22:38 [Dimob] Genome /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13, found formats: .faa .ffn .ptt
2022/07/22 16:22:38 [Dimob] Looking for mobility genes using hmmer
2022/07/22 16:22:38 [Dimob] Running hmmer command hmmscan /usr/local/opt/islandpath/hmmpfam/Pfam-A_mobgenes_201512_prok /home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/Taxa_98.13.faa >/home/gdouglas/tmp/dimob_tmpqZ6oLAAJ4V/blasttmpS0ynukKyPL
2022/07/22 16:22:39 [Dimob] Parsing hmmer results with Mobgene
2022/07/22 16:22:39 [Dimob::Mobgene] Using extended ids
2022/07/22 16:22:39 [Dimob] Retrieving mobility genes from ptt file
Use of uninitialized value in numeric eq (==) at /usr/local/opt/islandpath/lib/Dimob/tabdelimitedfiles.pm line 67.
2022/07/22 16:22:39 [Dimob] Calculating dinucleotide bias
Use of uninitialized value in concatenation (.) or string at /usr/local/opt/islandpath/lib/Dimob/genomicislands.pm line 372, <GEN7> line 181.
Use of uninitialized value in numeric eq (==) at /usr/local/opt/islandpath/lib/Dimob/tabdelimitedfiles.pm line 67.
2022/07/22 16:22:40 [Dimob] Looking for regions with dinuc bias and mobility genes
2022/07/22 16:22:40 [Dimob] Cleaning temporary files
2022/07/22 16:22:40 [Dimob] Cleaning up temp files for Dimob
2022/07/22 16:22:40 [main] Printing results
2022/07/22 16:22:40 [main] Removing tmp files
I am running into a few errors when trying to run islandpath on my own genbank files, but it worked on the example file. The files I'm working with are genbank files produced by prokka (which I think restricted to be single contigs by separating sections containing "//"). The errors I'm getting are similar to https://github.com/brinkmanlab/islandpath/issues/16 abd https://github.com/brinkmanlab/islandpath/issues/14, but I think those both were related to the genbank files containing multiple contigs.
You can see the code I'm using below, and I will attach the input genbank file I'm testing it out with.
(Again - the same command with
./NC_003210.gbkspecified instead worked fine)Is there something about the genbank format that I should be looking into? I think perhaps the ptt file is not being created properly, but I'm having a little trouble digging into that as I'm a singularity/docker novice.
This is the error/log output:
Thanks!
Gavin Taxa_98.13.gbk.gz