[Cg-pipeline-users] run_annotation_genbank.pl and compatibility with interproscan5

[Laure Q. <Lau...@if...>]

Hello,

do you plan to update cg-pipeline in order to handle interproscan5 xml 
output, which is different from interproscan4 ?

I also have the error below, do you have an idea of the problem ?
ANNOTATION GENBANK FILE CREATION START on cgtest Tue Jun 25 19:20:04 
(CG-Pipeline v0.4.0.0)
COMMAND
   run_annotation_genbank.pl --organism=cgtest 
--prediction=/mnt/data2/home1/lquintri/cgtest/prediction.gb 
--inputdir=/mnt/data2/home1/lquintri/cgtest/annotation 
--gb=/mnt/data2/home1/lquintri/cgtest/annotation.gb 2>&1 |tee --append 
cgtest/log/genbank.txt
run_annotation_genbank.pl: main::main: Putting all annotations in 
/mnt/data2/home1/lquintri/cgtest/annotation into memory
run_annotation_genbank.pl: main::main: Transforming the prediction 
genbank into a set of features
run_annotation_genbank.pl: main::readSqlFile: TID3 
/mnt/data2/home1/lquintri/cgtest/annotation/aa.fasta.card_hits.sql

--------------------- WARNING ---------------------
MSG: exception while parsing location line [1..25250] in reading 
EMBL/GenBank/SwissProt, ignoring feature source 
(seqid=NODE_100_length_25148_cov_343.557709): Eval-group not allowed at 
runtime, use re 'eval' in regex m/(.*?)\(((?x-ism:
                 (?>
                 [^()]+
                 |
                 \(
                 (??{.../ at 
/home12/caparmor/bioinfo/softs/perlmodules/lib/perl5/Bio/Factory/FTLocationFactory.pm 
line 160, <GEN0> line 14.

---------------------------------------------------
Thread 2 terminated abnormally: Can't call method "primary_tag" on an 
undefined value at 
/home12/caparmor/bioinfo/softs/perlmodules/lib/perl5/Bio/SeqIO/genbank.pm line 
687, <GEN0> line 14.
Can't use an undefined value as an ARRAY reference at 
/mnt/data/home12/bioinfo/softs/sources/cgp/scripts/run_annotation_genbank.pl 
line 43.
Perl exited with active threads:
	2 running and unjoined
	-1 finished and unjoined
	0 running and detached
ANNOTATION GENBANK END on cgtest Tue Jun 25 19:20:04 (CG-Pipeline v0.4.0.0)

Thank you,
Regards,
Laure