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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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genomes in directory not used? #96

Closed maguileraf closed 2 years ago

maguileraf commented 2 years ago

I have 100 genomes in my directory but parsnp only analyzes 8 and I can't figure out why.

bkille commented 2 years ago

Hi @maguileraf,

Can you provide some more details? Please provide the full Parsnp command used as well as all output, for example: 

blk6@sno:~/Projects/HarvestSuite/parsnp$ ./parsnp -r! -d examples/mers_virus/genomes/*.fna --out mers_demo
|--Parsnp 1.5.6--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
Ref !
13:39:38 - INFO - 
**************************
SETTINGS:
|-refgenome:    autopick
|-genomes:  
    examples/mers_virus/genomes/Al-Hasa_1_2013.fna
    examples/mers_virus/genomes/Al-Hasa_12_2013.fna
    ...44 more file(s)...
    examples/mers_virus/genomes/Taif_1_2013.fna
    examples/mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna
|-aligner:  muscle
|-outdir:   mers_demo
|-OS:   Linux
|-threads:  1
**************************

13:39:38 - INFO - <<Parsnp started>>
13:39:38 - INFO - No genbank file provided for reference annotations, skipping..
13:39:38 - ERROR - File examples/mers_virus/genomes/Al-Hasa_ALL.fna is 8.92x longer than reference! Skipping...
13:39:38 - INFO - Recruiting genomes...
13:39:39 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner...
13:39:39 - INFO - Reconstructing core genome phylogeny...
13:39:43 - INFO - Aligned 48 genomes in 1.43 seconds
13:39:43 - INFO - Parsnp finished! All output available in mers_demo
maguileraf commented 2 years ago

I used the wrong file as reference

bkille commented 2 years ago

Great, let me know if you have any further issues!