PopCOGenT
PopCOGenT copied to clipboard
philarevalo
PopCOGenT
Im running into an error copy pasted below. I am running PopCOGenT on 3 assemblies
Ouput directory does not exist. Creating new directory. Traceback (most recent call last): File "/GWSPH/groups/liu_price_lab/tools/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1618, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1626, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'Larger genome'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "cluster.py", line 315, in
Hello! I think the problem is that your 3 genomes only formed a single clonal cluster, i.e., they were all too closely related to infer population structure by gene flow. If you share the contents of your *length_bias.txt file, I can confirm.
Thankyou for responding so quickly.. the 'FUTI_PopCOGenT.length_bias.txt ' is actually empty.. is there a log that I can check to see if the code doesnt like something or missing some inputs?
[mlaziz@log003 PopCOGenT]$ cat output/FUTI_PopCOGenT.length_bias.txt Strain 1 Strain 2 Initial divergence Alignment size Genome 1 size Genome 2 size Observed SSD SSD 95 CI low SSD 95 CI high
Unfortunately there isn't a logfile at the moment, but I will get back to you on what might be going on.
im running the tool on the university's HPC. There are a lot of files in /proc. Are you looking for any one particular file?
Hi,
I got exactly the same error, then I checked the steps and found in the script get_alignment_and_length_bias.py there is one lineglob.glob(genome_directory + '*' + genome_extension) which assumes your genome_directory ends with / to work properly, so first you need to give it like this genome_dir=genomes/ in the config.sh file.
If it still doesn't work, that's probably because your mugsy wasn't configured properly. You probably need to modify the export MUGSY_INSTALL=./mugsy_x86-64-v1r2.3 line to the absolute path in the mugsyenv.sh file.
Hope it helps.
Best, Shengwei
@maziz2 if the solution that @housw suggested doesn't work, a useful file from proc to see would be any *.txt file. In theory, there should have been one created for each alignment. If there are no *.txt files, then I suspect that the above solution will work.
