problems with genbank file
I have problems creating a reconstruction with pathwaystools (21.0) when it comes to this genbank file (download: ufile.io/m73yj).
The annotation was created with gamola2 and is very comprehensive (10mb as archive). If I use pathwaytools to create a new pgdb with this file, then the program stops with the following errors:
Created myb71_gamolacyc directory tree.
Saved /home/jo/local/software/ptools-local/pgdbs/user/myb71_gamolacyc/1.0/input/organism.dat
Saved /home/jo/local/software/ptools-local/pgdbs/user/myb71_gamolacyc/1.0/input/organism-init.dat
Copying class Organisms from METABASE to MYB71_GAMOLABASE.
[Copying class hierarchy into MYB71_GAMOLABASE]
[Completed initialization of new PGDB for MYB71_GAMOLA]
[Saving KB MYB71_GAMOLABASE to V4-FASL file /home/jo/local/software/ptools-local/pgdbs/user/myb71_gamolacyc/1.0/kb/myb71_gamolabase.ocelot
0 frames ignored
9500 frames saved]
[Saving KB PGDB-METADATA to V1-SEXPR file /home/jo/local/software/ptools-local/pgdbs/user/PGDB-METADATA.ocelot
0 frames ignored
1 frames saved]
Copying /tmp/tmp.PPQyqRjqrR/unnamed.0.gbk to organism input directory
[Processed 5 data rows from file /home/jo/local/software/ptools-local/pgdbs/user/myb71_gamolacyc/1.0/input/genetic-elements.dat]
[Processed 1 data frames]
;;; Error:
Parse error in the GenBank Feature entry above line 17775
in file /home/jo/local/software/ptools-local/pgdbs/user/myb71_gamolacyc/1.0/input/unnamed.0.gbk
Examine this entry in the file for syntactic or formatting errors.
The error message was:
`NIL' is not of the expected type `NUMBER'
batch-pathologic: A fatal error occurred for ./ version 1.0.
See pathologic log file ./pathologic.log for more details.
21-Oct-2017 15:50:50 Fatal error: `NIL' is not of the expected type `NUMBER'
Evaluation stack:
; Autoloading for DISASSEMBLE:
; Fast loading from bundle private/disasm.fasl.
; Fast loading from bundle code/x/disx86-64.fasl.
->(TPL::ZOOM-COMMAND :FROM-READ-EVAL-PRINT-LOOP NIL ...)
(SYS::..RUNTIME-OPERATION "applyn" :UNKNOWN-ARGS)
(TPL:DO-COMMAND "zoom" :FROM-READ-EVAL-PRINT-LOOP ...)
The feature above line 17775 in the genbank file is:
PFAM_match complement(141859..142236)
/label="Opacity"
/note="both ends of the alignment ended internally"
/note="Cumulative evalue for family Opacity: 2.4e-07"
/pfam_match="02462: Opacity family porin protein:
Pathogenic Neisseria spp. possess a repertoire of phase-
variable Opacity proteins that mediate various pathogen--
host cell interactions. These proteins are integral
membrane proteins related to other porins."
/interpro="IPR003394: Pathogenic Neisseria spp. possess a
repertoire of phase-variable opacity proteins that mediate
various pathogen/host cell interactions [PUBMED:10036728].
These proteins are integral membrane proteins related to
other porins and the OpA protein."
/product="Opacity, Opacity family porin protein Score=23.1
Expect=5.5e-05"
What is going wrong?