list index out of range with srst2.py

[anuravi1234]

Hello, I am trying to run the getmlst.py script. This is the command I am using:
python2 /mnt/volume_2/srst2/scripts/srst2.py --input_se 669_EF_MAG_EF_MAG.fastq --output 582_mlst --log --mlst_db /mnt/volume_2/srst2/Enterococcus_faecium.fasta --mlst_definitions /mnt/volume_2/srst2/efaecium.txt --read_type q

The sam output and bowtie files were created but when i got this error in the last step of the process, I am not sure how to solve it.
Traceback (most recent call last):
File "/mnt/volume_2/srst2/scripts/srst2.py", line 1773, in
main()
File "/mnt/volume_2/srst2/scripts/srst2.py", line 1717, in main
mlst_report, mlst_results = run_srst2(args, fileSets, args.mlst_db, "mlst")
File "/mnt/volume_2/srst2/scripts/srst2.py", line 1264, in run_srst2
db_results_list, fasta)
File "/mnt/volume_2/srst2/scripts/srst2.py", line 1327, in process_fasta_db
results,gene_list, db_report, cluster_symbols, max_mismatch)
File "/mnt/volume_2/srst2/scripts/srst2.py", line 1429, in map_fileSet_to_db
size_allele, next_to_del_depth_allele, run_type,unique_gene_symbols, unique_allele_symbols)
File "/mnt/volume_2/srst2/scripts/srst2.py", line 510, in score_alleles
unique_gene_symbols,unique_allele_symbols)
File "/mnt/volume_2/srst2/scripts/srst2.py", line 931, in group_allele_dict_by_gene
gene_name = get_allele_name_from_db(allele,run_type,args,unique_allele_symbols,unique_cluster_symbols)[component_ind]
File "/mnt/volume_2/srst2/scripts/srst2.py", line 900, in get_allele_name_from_db
allele_name = gene_name[1]
IndexError: list index out of range

Thank you for helping!

Anu

[josemunozc]

Same problem here

[sazal-mib]

same problem :(

[thomasmulvaney]

Depending on MLST scheme, you might need to specify the delimiter with -mlst_delimiter. For example I had to use -mlst_delimiter '_' for S. pneumoniae. That seemed to fix the issue for me.