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Arkadiy-Garber / FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
GNU Affero General Public License v3.0
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running programm with reference database for blast searches throws error #46

Open ckeuschn opened 4 months ago

ckeuschn commented 4 months ago

Hi,

When I run the program providing a reference database it throws an error which I cannot figure out how to solve. Any help is appreciated!

Cheers, Christoph

/Final processing of output

Traceback (most recent call last): File "/home/ckeuschn/miniconda3/envs/fegenie/bin/FeGenie.py", line 3020, in main() File "/home/ckeuschn/miniconda3/envs/fegenie/bin/FeGenie.py", line 2355, in main ls[0] + "," + ls[1] + "," + str(idxDict[ls[2]]) + "," + ls[3] + "," + ls[4] + "," + ls[ ^^^^^^^ UnboundLocalError: cannot access local variable 'idxDict' where it is not associated with a value /

Arkadiy-Garber commented 4 months ago

Hi Christoph,

Thanks for your interest in FeGenie, and apologies for the delayed response.

Thanks for sharing that error output. Could you please send me the command that you are using to invoke FeGenie?

Thanks, Arkadiy

ckeuschn commented 2 weeks ago

Hi Arkadiy,

sorry I missed your response here an I am back now on this again. I have still problems with running the programm with a refDB. this is my command:

FeGenie.py \ -bin_dir .\ -bin_ext faa \ -out fegenie_out_uniprot \ --orfs \ -t 16\ -ref /home/ckeuschn/databases/uniprot_sprot.fasta

but that gives me an empty output file now:

head FeGenie-summary.csv category,genome,assembly,orf,HMM,bitscore,bitscore_cutoff,cluster,heme_binding_motifs,top_blast_hit,blast_hit_evalue,protein_sequence

,#,#,#,#,#,#,

,#,#,#,#,#,#,

,#,#,#,#,#,#,

,#,#,#,#,#,#,

,#,#,#,#,#,#,

When I run it without a database I get a table with hits and everything. what am I missing here?
Thanks a lot!