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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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no tree calculated #58

Closed Roman-G1 closed 4 years ago

Roman-G1 commented 5 years ago

Using the provided MERS and S. pneumoniae data sets parsnp fails to create a tree:

xyz@sebio05:~/parsnp$ parsnp -r ./strep31/NC_011900.fna -d
 ./strep31 -p 40 -c -x
 |--Parsnp v1.2--|
 For detailed documentation please see --> 
 http://harvest.readthedocs.org/en/latest
 ****************************************************************
 SETTINGS:
 |-refgenome:   ./strep31/NC_011900.fna
 |-aligner: libMUSCLE
 |-seqdir:  ./strep31
 |-outdir:  /home/gerlachr/parsnp/P_2018_11_30_134606501169
 |-OS:      Linux
 |-threads: 40
 ****************************************************************

 <<Parsnp started>>

 -->Reading Genome (asm, fasta) files from ./strep31..
   |->[OK]
 -->Reading Genbank file(s) for reference (.gbk) ..
   |->[WARNING]: no genbank file provided for reference annotations, 
 skipping..
 -->Running Parsnp multi-MUM search and libMUSCLE aligner..
   |->[OK]
 -->Running PhiPack on LCBs to detect recombination..
   |->[OK]
 -->Reconstructing core genome phylogeny..
 Traceback (most recent call last):
   File "/usr/bin/parsnp", line 1176, in <module>
     tree.reroot_at_midpoint(update_splits=False)
TypeError: reroot_at_midpoint() got an unexpected keyword argument 
'update_splits'

parsnp 1.2 was installed on Debian 9 using the Debian Med package . Any idea? Thanks in advance and best, Roman

bkille commented 4 years ago

Im assuming this had to do with the dendropy python package. The keyword should have been update_bipartition. This has been fixed now.