search

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
53 stars 10 forks source link

Error when cluster ORFs #20

Open Rachael-16 opened 3 years ago

Rachael-16 commented 3 years ago

Hi there,

I've run into a new problem with running FeGenie. Previously I've run the script with no issue however now I receive the following error everytime I try to run

Consolidating summary files into one master summary file Identifying genomic proximities and putative operons Clustering ORFs... Looking for Thermincola S-layer cytochromes and Geobacter-related porin-cytochrome operons Pre-processing of final outout file rm: cannot remove 'fegenie_out4/GeoThermin.csv': Text file busy rm: cannot remove 'fegenie_out4/magnetosome_formation-summary.csv': Text file busy rm: cannot remove 'fegenie_out4/FinalSummary-dereplicated-clustered-blast.csv': Text file busy rm: cannot remove 'fegenie_out4/Afreen_L.plantarum202195_GCA_010586945.1_ASM1058694v1_genomic.fna-thermincola.blast': Text file busy Counting heme-binding motifs rm: cannot remove 'fegenie_out4/FeGenie-summary.csv': Text file busy mv: cannot move 'fegenie_out4/FeGenie-summary-blasthits.csv' to 'fegenie_out4/FeGenie-summary.csv': Operation not permitted Final processing of output Traceback (most recent call last): File "/home/qiime/FeGenie/FeGenie.py", line 2719, in <module> main() File "/home/qiime/FeGenie/FeGenie.py", line 1596, in main if ls[6] != "cluster": IndexError: list index out of range

I see that updates were made to the FeGenie.py script 27 days ago I'm assuming this may be a an error do to the addition of some categories, however I'm not sure how to troubleshoot it. Any help you can offer would be appreciated.

Thanks

Arkadiy-Garber commented 3 years ago

Hi Rachael,

Thanks for using FeGenie. I did make some changes about a month ago, but have tested the program since then and it appears to finish without any errors for me.

Are you running FeGenie on a server? My suspicion is that this error is caused by the fact that the server running this program does not have time to propagate files to the NFS. So when FeGenie attempts to remove or re-name old files, it fails, eventually resulting in a crash because the right file-names are not present in the output directory.

To try to resolve this, I added to the program instructions to wait 5 seconds every time a new file is written and closed. Hopefully, this should fix the issue. But if not, let me know, and I will look further into this. It is possible that re-naming some categories caused some kind of bugged that was undetectable in my benchmarking. But that error does not look to be caused by that.

Thanks, Arkadiy