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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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CGC-Finder Error: list index out of range #45

Closed szzxpxf closed 4 years ago

szzxpxf commented 4 years ago

Dear developer, I can run the dbCAN2 tool without any issue when not using the CGC finder. However, when I specify a gff file with the "-c" option, I got the following error:

*****CGC-Finder start**** Traceback (most recent call last): File "~/miniconda3/envs/run_dbcan/bin/run_dbcan.py", line 391, in notes[temp[0]] = temp[1] IndexError: list index out of range

Could you let me know what I can do to fix this?

Thank you!

linnabrown commented 4 years ago

@szzxpxf What does the last column of your gff file look like? We assume that your input gff file is the standard gff3 format. That is, the last column is {key}={value};{key}={value};...

szzxpxf commented 4 years ago

This is the last field of my gff file: ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.291;conf=100.00;score=98.24;cscore=100.55;sscore=-2.31;rscore=-4.86;uscore=-0.38;tscore=2.93;

szzxpxf commented 4 years ago

It's generated from prodigal. Do I need to trim down the number of fields? Or do you recommend another gene-calling tool? These are metagenome-assembled genomes.

linnabrown commented 4 years ago

delete the ";" at the end of the in you gff file solve this problem.

linnabrown commented 4 years ago 
pip install run-dbcan==2.0.11

to save your life. I solve the prodigal problem now.

szzxpxf commented 4 years ago

Thanks so much for fixing this!!! I could have delete the extra ; at the end of the gff file. I'm sure many other future users will benefit from this update in case they have gff generated from prodigal!

Rob-murphys commented 1 year ago

A similar error has come up again from gff format files created by prodigal.