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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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IndexError during Final processing of output #9

Closed zreitz closed 4 years ago

zreitz commented 4 years ago

Running the quick-start fasta files directly following a conda install gives the following error:

FeGenie.py -bin_dir test_pao1/ -bin_ext txt -t 1
checking arguments
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.
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All required arguments provided!

Finding ORFs for Pseudomonas_aeruginosa_PA01.txt
starting main pipeline...

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Looking for following iron-related functional category: iron_aquisition-heme_oxygenase
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

.
Looking for following iron-related functional category: iron_aquisition-heme_transport
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

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Looking for following iron-related functional category: iron_aquisition-iron_transport
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

.
Looking for following iron-related functional category: iron_aquisition-siderophore_synthesis
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

.
Looking for following iron-related functional category: iron_aquisition-siderophore_transport
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

.
Looking for following iron-related functional category: iron_gene_regulation
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

.
Looking for following iron-related functional category: iron_oxidation
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

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Looking for following iron-related functional category: iron_reduction
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

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Looking for following iron-related functional category: iron_storage
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

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Looking for following iron-related functional category: magnetosome_formation
analyzing Pseudomonas_aeruginosa_PA01.txt: 100%   

Consolidating summary files into one master summary file
Identifying genomic proximities and putative operons
Clustering ORFs...

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Looking for Thermincola S-layer cytochromes and Geobacter-related porin-cytochrome operons
Pre-processing of final outout file
Counting heme-binding motifs
Final processing of output

Traceback (most recent call last):
  File "/home/snip/FeGenie/FeGenie.py", line 2167, in <module>
    main()
  File "/home/snip/FeGenie/FeGenie.py", line 1414, in main
    memoryDict[dataset][orf]["seq"] = ls[10]
IndexError: list index out of range

Platform: Debian 10 Python 3.7.6

Arkadiy-Garber commented 4 years ago

Hi,

Thanks for using FeGenie, and for bringing my attention to this issue! This error stemmed from a small bug in the script that was just fixed. Apologies for the inconvenience.

Feel free to re-run the program after a new git clone https://github.com/Arkadiy-Garber/FeGenie.git

Thanks, Arkadiy

zreitz commented 4 years ago

Thank you! That fixed the issue.