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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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IndexError: list index out of range #13

Closed gchevignon closed 2 years ago

gchevignon commented 3 years ago

Hello,

I have tried to run eukcc on a protein dataset but I got this error:

eukcc --db /home1/datawork/gchevign/Data.dir/eukcc_db.dir/eukccdb/ --outdir /home1/datawork/gchevign/Bonamia_RNAseq.dir --ncores 2 --proteins /home1/datawork/gchevign/Bonamia_RNAseq.dir/7-annotation.dir/1-transdecoder.dir/Trinity_2.fasta.transdecoder_clean.pep

11/27/2020 13:27:58: Starting EukCC 11/27/2020 13:28:02: MAG succesfully placed in tree 11/27/2020 13:28:02: Using pressed hmms from last run 11/27/2020 13:28:02: 294381 taxid not found Traceback (most recent call last): File "/home1/datawork/gchevign/Soft.dir/eukcc/bin/eukcc", line 10, in sys.exit(main()) File "/home1/datawork/gchevign/Soft.dir/eukcc/lib/python3.6/site-packages/eukcc/main.py", line 222, in main _ = m.inferLineage(m.placements[m.cfg["placementMethod"]]) File "/home1/datawork/gchevign/Soft.dir/eukcc/lib/python3.6/site-packages/eukcc/workflow.py", line 306, in inferLineage common = set(lngs[0]) IndexError: list index out of range

openpaul commented 3 years ago

I could not reproduce this bug, could you supply me with your dataset? Maybe the bug was already solved in the newest version (0.3)?

diedie9 commented 2 years ago

Hello, I also have this error when run eukcc. Do you debug it ? My eukcc version is 3.2

04/02/2022 14:03:28: Starting EukCC - yes 04/02/2022 14:03:28: Running GeneMark-ES 04/02/2022 15:08:29: Extracting protein locations 04/02/2022 15:08:29: Searching for proteins to place in the tree 04/02/2022 15:08:41: Processing Hmmer results 04/02/2022 15:08:48: Placing proteins in tree 04/02/2022 15:13:40: MAG succesfully placed in tree 04/02/2022 15:13:40: 378 hmm profiles need to be used for estimations 04/02/2022 15:13:40: Concatenating hmms, this might take a while (IO limited) 04/02/2022 15:13:48: Pressing hmms 04/02/2022 15:13:50: Running hmmer for chosen locations 04/02/2022 15:15:39: Processing Hmmer results 04/02/2022 15:15:39: 667725 taxid not found Traceback (most recent call last): File "/data/msb/tools/eukcc/eukcc_env/bin/eukcc", line 8, in sys.exit(main()) File "/data/msb/tools/eukcc/eukccenv/lib/python3.7/site-packages/eukcc/main.py", line 222, in main = m.inferLineage(m.placements[m.cfg["placementMethod"]]) File "/data/msb/tools/eukcc/eukcc_env/lib/python3.7/site-packages/eukcc/workflow.py", line 261, in inferLineage common = set(lngs[0]) IndexError: list index out of range

openpaul commented 2 years ago

I believe you are using EukCC version 1 (3.2 was never released [Not consciously at least], so maybe its 0.3.2), the latest version is EukCC 2, which should be used.

I am not maintaining the old 1 version anymore.

I recommend using the latest docker container, which should make installation fast and easy. Please make sure to fetch the latest database as well, as the old one does not work with the new update.

https://github.com/Finn-Lab/EukCC