name 'chr_spos' is not defined in parsnp

marbl / parsnp

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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name 'chr_spos' is not defined in parsnp #87

Closed ruchi19flowchart closed 3 years ago

ruchi19flowchart commented 3 years ago

12:02:28 - INFO - <> 12:02:28 - INFO - No genbank file provided for reference annotations, skipping.. 12:02:29 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 12:08:06 - INFO - Running PhiPack on LCBs to detect recombination... Traceback (most recent call last): File "/opt/app/anaconda/bin/parsnp", line 1321, in if block_spos < chr_spos:

the above error I'm getting when I'm executing the program taking multifasta file as a reference. Running 1.5.3 version. Kindly check.

bkille commented 3 years ago

@ruchi19flowchart Hi! Thanks for bringing this bug to attention and sorry for the inconvenience. There is a new release available (also on bioconda) that should resolve this issue. Note that bioconda version does not have an updated version string (running parsnp --version will still show 1.5.3), however through conda you can verify that the version is indeed 1.5.4. I will be fixing this tonight, though.

ruchi19flowchart commented 3 years ago

Thank you so much