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Error when running example script EToKi.py MLSTdb

Open theInnuendoProject opened this issue 3 years ago • 0 comments

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?

theInnuendoProject avatar Jul 29 '20 20:07 theInnuendoProject