Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error when running example script EToKi.py MLSTdb #8

Open
theInnuendoProject opened this issue Jul 29, 2020 · 0 comments
Open

Error when running example script EToKi.py MLSTdb #8

theInnuendoProject opened this issue Jul 29, 2020 · 0 comments

Comments

@theInnuendoProject
Copy link

Hello,
I installed EToKi and tried the example as showed in the README file but I got the following error.

./EToKi.py MLSTdb -i examples/Escherichia.Achtman.alleles.fasta -r examples/Escherichia.Achtman.references.fasta -d examples/Escherichia.Achtman.convert.tab
2020-07-29 20:45:04.997470 Exemplar sequences in ./NS_2085r4ap/clsFna.clust.exemplar
2020-07-29 20:45:04.997569 Clusters in ./NS_2085r4ap/clsFna.clust.tab
2020-07-29 20:45:05.030599 Run BLASTn starts
2020-07-29 20:45:05.384751 Run BLASTn finishes. Got 971 alignments
2020-07-29 20:45:05.384888 Run diamond starts
2020-07-29 20:45:06.047658 Run diamond finishes. Got 966 alignments
2020-07-29 20:45:06.375628 removed 0 paralogous sites.
2020-07-29 20:45:06.375682 obtained 5530 alleles and 39 references alleles
2020-07-29 20:45:06.378881 A file of reference alleles has been generated: examples/Escherichia.Achtman.references.fasta
Traceback (most recent call last):
File "EToKi.py", line 47, in
etoki()
File "EToKi.py", line 41, in etoki
eval(arg.cmd)(sys.argv[2:])
File "/mnt/data/disk1/biotools/EToKi/modules/MLSTdb.py", line 164, in MLSTdb
conversion[0].append(get_md5(allele['value']))
TypeError: string indices must be integers

I installed in a conda env with python 3.6.
Some ideas how to fix it?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant