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problems with genbank file

asked 2017-10-21 09:11:40 -0600

jo gravatar image

updated 2017-10-21 09:31:54 -0600

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?

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answered 2017-10-30 22:26:20 -0600

kr gravatar image

Hi, apologies for the delay in replying. This was somewhat tricky to track down, but it clealry was a parser bug. Thanks for reporting this.

I issued patch p3843-pl-gbk-parser-fq.fasl for 21.0 , which should fix this.

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Asked: 2017-10-21 09:11:40 -0600

Seen: 19 times

Last updated: Oct 30