cdhit_to_csv.py and IndexError: list index out of range

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens

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cdhit_to_csv.py and IndexError: list index out of range #89

Closed TreeT2 closed 3 years ago

TreeT2 commented 7 years ago

Hi All,

Im trying to setup a database for analysis using instructions on https://github.com/katholt/srst2#clusteringsequences I get as far as step 2 before I get the following error

my fasta header look like:

Thanks

katholt commented 7 years ago

This error is in reading the cluster file (.clstr) output by cd-hit-est, not the fasta file. Are you passing the right output from cd-hit-est to the script via --cluster_file ?