search

brinkmanlab / islandpath

IslandPath standalone software
GNU General Public License v3.0
31 stars 4 forks source link

hmmpfam hmm file error #11

Closed myshu2017-03-14 closed 3 years ago

myshu2017-03-14 commented 4 years ago

Hi, After I install the software and run the example, there was an error as follow:

Error: Unrecognized format, trying to open hmm file /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/hmmpfam/Pfam-A_mobgenes_201512_prok for reading.

How to fix it? Can you help me? Looking for your reply! Thank you very much! best wishes, myshu

myshu2017-03-14 commented 4 years ago

I solved the error! Just set the command hmmscan of Dimob.config using abslute directory! But when I run the example, the log as follow, and still had some warnings, such as Use of uninitialized value in numeric eq (==) , is that matters?

Smartmatch is experimental at /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/lib/GenomeUtils.pm line 666. Smartmatch is experimental at /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/lib/GenomeUtils.pm line 669. Smartmatch is experimental at /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/lib/GenomeUtils.pm line 844. /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/logger.conf2019/11/20 17:07:33 [main] Logging initialized 2019/11/20 17:07:33 [main] Creating temp directory with needed files 2019/11/20 17:07:33 [main] This is the /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210 2019/11/20 17:07:33 [GenomeUtils] From filename /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210.gbk got /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210, gbk 2019/11/20 17:07:33 [GenomeUtils] Reading genbank format file 2019/11/20 17:07:33 [GenomeUtils] The genome sequence in /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210.gbk has been read. 2019/11/20 17:07:35 [GenomeUtils] Checking contig NC_003210 2019/11/20 17:07:35 [GenomeUtils] Found sequence in the genbank/embl file 2019/11/20 17:07:35 [GenomeUtils] We have 1 contigs 2019/11/20 17:07:35 [GenomeUtils] From filename /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210.gbk got /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210, gbk 2019/11/20 17:07:35 [GenomeUtils] No base filename given in args, trying to use object default: /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210 2019/11/20 17:07:35 [GenomeUtils] Found formats: 2019/11/20 17:07:35 [GenomeUtils] The genome sequence in /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210.gbk has been read. 2019/11/20 17:07:35 [GenomeUtils] Now generating required file formats (faa, ffn and ptt) 2019/11/20 17:07:39 [GenomeUtils] No base filename given in args, trying to use object default: /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210 2019/11/20 17:07:39 [main] Running IslandPath-DIMOB 2019/11/20 17:07:39 [Dimob] Genome /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210, found formats: .faa .ffn .ptt 2019/11/20 17:07:39 [Dimob] Looking for mobility genes using hmmer 2019/11/20 17:07:39 [Dimob] Running hmmer command /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/hmmer-3.1b1/bin/hmmscan /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/hmmpfam/Pfam-A_mobgenes_201512_prok /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/NC_003210.faa >/ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/example/dimob_tmpZZ3y34cH5F/blasttmpOJfRJAa6rV 2019/11/20 17:08:19 [Dimob] Parsing hmmer results with Mobgene 2019/11/20 17:08:19 [Dimob::Mobgene] Using extended ids 2019/11/20 17:08:22 [Dimob] Retrieving mobility genes from ptt file Use of uninitialized value in numeric eq (==) at /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/lib/Dimob/tabdelimitedfiles.pm line 67. 2019/11/20 17:08:22 [Dimob] Calculating dinucleotide bias Use of uninitialized value in concatenation (.) or string at /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/lib/Dimob/genomicislands.pm line 372, line 2867. Use of uninitialized value in numeric eq (==) at /ifswh1/BC_COM_P11/P3/F18FTSECWLJ1207/software/islandpath/lib/Dimob/tabdelimitedfiles.pm line 67. 2019/11/20 17:08:38 [Dimob] Looking for regions with dinuc bias and mobility genes 2019/11/20 17:08:38 [Dimob] Cleaning temporary files 2019/11/20 17:08:38 [Dimob] Cleaning up temp files for Dimob 2019/11/20 17:08:38 [main] Printing results 2019/11/20 17:08:38 [main] Removing tmp files

innovate-invent commented 3 years ago

Sorry for the very late reply. I don't believe this matters, it is warning about an implicit cast that likely should be fixed at some point.