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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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Fail to force inclusion of all genomes #104

Closed zjshi closed 2 years ago

zjshi commented 2 years ago

Hi, I have been running Parsnp v1.2 on a set of 50 bacterial genomes.

Here is the command line I used:

parsnp -c -d 102492_50/ -r ./102492_ref.fna

Despite supplying -c flag, Parsnp appears to only use a small subset of input genomes (n=13). Please see the detailed program output below. Thanks in advance for any help you may provide!

|--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

SETTINGS: |-refgenome: ./102492_ref.fna |-aligner: libMUSCLE |-seqdir: 102492_50/ |-outdir: /raid1/P_2022_01_26_071302778873 |-OS: Linux |-threads: 32

<>

-->Reading Genome (asm, fasta) files from 102492_50/.. |->[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.. |->[SKIP] -->Reconstructing core genome phylogeny.. |->[OK] -->Creating Gingr input file.. |->[OK] -->Calculating wall clock time.. |->Aligned 13 genomes in 36.94 seconds

<<Parsnp finished! All output available in /raid1/P_2022_01_26_071302778873>>

Validating output directory contents... 1)parsnp.tree: newick format tree [OK] 2)parsnp.ggr: harvest input file for gingr (GUI) [OK] 3)parsnp.xmfa: XMFA formatted multi-alignment [OK]

bkille commented 2 years ago

Hi @zjshi! Thanks for opening the issue. Parsnp v1.2 is no longer supported, could you update to v1.6 and let me know if the issue persists? Thanks!

To install from conda, you'll need to make sure that your channels are updated.

zjshi commented 2 years ago

@bkille Yes, this issue is not with higher versions of Parsnp. Thanks!