[Gmod-schema] [Chado automation] Issues with bash calls

[RAJAONISON A. <mir...@ya...>]

Hi all,

 

It seems like i can't use chado gmod_bulk_load inside a bash script even. 

 

Can someone enlighten me on that ? 

 

Thank you for in advance

 

Miharimamy

 

I get the following when I execute this command : 

 

$ chado-1.31/load/bin/gmod_bulk_load_gff3.pl --organism "acinetobacter"
--gfffile
acinetobacter/GCF_000018445.1/GCF_000018445.1_ASM1844v1_genomic.gff.sorted
-fastafile
acinetobacter/GCF_000018445.1/GCF_000018445.1_ASM1844v1_genomic.fna --dbname
chado --dbuser chadousr --dbpass <password>

 

 

DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 1209, <GEN0> line 2.

"acinetobacter" organism not found in the database at
/home/bee/chado-1.31/load/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line
2.

 

Abnormal termination, trying to clean up...

 

Trying to remove the run lock (so that --remove_lock won't be needed)...

Exiting...

 

The same command gives executed in my current shell gives me :

 

Unable to find srcfeature NC_010611.1 in the database.

Perhaps you need to rerun your data load with the '--recreate_cache' option.
at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 2.

 
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x2a9
b0f8)', 'Bio::SeqFeature::Annotated=HASH(0x2cfae70)') called at
chado-1.31/load/bin/gmod_bulk_load_gff3.pl line 851

 

Abnormal termination, trying to clean up...

 

Attempting to clean up the loader temp table (so that --recreate_cache

won't be needed)...

Trying to remove the run lock (so that --remove_lock won't be needed)...

Exiting...