Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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TypeError: '<' not supported between instances of 'int' and 'list' #102
Hello,
I have conda version of parsnp 1.5.6
I try to take the reference with 5 contigs and have the same issue as in #87.
when I took only the first contig that contains chromosome, everything worked without errors.
Traceback (most recent call last):
File "/home/miniconda3/envs/parsnp/bin/parsnp", line 1328, in <module>
if block_spos < chr_spos:
Hi @valery-shap, thanks for pointing this out to us! The most recent version of parsnp, 1.6.1, should have this bug fixed. Please let me know if it is still an issue after updating.
bkille
commented
2 years ago 
valery-shap
Hello, I have conda version of parsnp 1.5.6 I try to take the reference with 5 contigs and have the same issue as in #87. when I took only the first contig that contains chromosome, everything worked without errors.
Best regards, Valery