Comments (2)
Same here. I run get_sequence_type
for 1108 Helicobacter pylori assemblies, 530 resulted in concatenated all N fasta files. I inspected the assembly information of the strains, found that the error happens when the contig number is low (<20) or not many Ns in the assembly result (< 1000). For example, 25 complete genome assemblies all failed. Eight of them are in the attachment.
complete_hpylori.zip
from mlst_check.
I have the same error.
from mlst_check.
Related Issues (13)
- Issue with running get_sequence_type HOT 1
- Licence HOT 1
- Something went wrong, got a 500 status code at /usr/local/share/perl/5.22.2/Bio/MLST/Download/Downloadable.pm line 24. HOT 1
- download_mlst_databases Could not connect to https://pubmlst.org/data/dbases.xml HOT 1
- url not found HOT 2
- Different order of MLST alleles to Leptospira
- readdir() attempted on invalid dirhandle HOT 1
- Perl Error while running download_mlst_databases
- No results from get_sequence_type HOT 5
- mlst database
- get_sequence_type -s "Pseudomonas aeruginosa" *.fna Can't locate Bio/Perl.pm in @INC (you may need to install the Bio::Perl module)
- Unable to download database
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