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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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Parsnp requires 2 or more genomes to run, exiting #152

Closed yissachar17 closed 2 months ago

yissachar17 commented 2 months ago

I run this yesterday evening with no problems at all. Everything worked perfectly. Unfortunately, the generated files weren't saved so I tried it again. Now I am getting the below issue Parsnp requires 2 or more genomes to run, exiting. Please help. I need this to build a phylogenetic tree. Thanks in advance

parsnp -r referenceGenome/sequence\ (1).fasta -d genomes/*.fasta -o parsnpFiles

08:12:32 - INFO - |--Parsnp 2.0.5--|

08:12:32 - INFO -

SETTINGS: |-refgenome: referenceGenome/sequence (1).fasta |-genomes: genomes/174_assembly.fasta genomes/198_assembly.fasta ...2 more file(s)... genomes/66_assembly.fasta genomes/93_assembly.fasta |-aligner: muscle |-outdir: parsnpFiles |-OS: Linux |-threads: 1

08:12:32 - INFO - <> 08:12:32 - INFO - No genbank file provided for reference annotations, skipping.. 08:12:32 - INFO - Recruiting genomes... 08:13:48 - ERROR - MUMi file generation failed... use all? 08:13:48 - INFO - Too few genomes to run partitions of size >50. Running all genomes at once. 08:13:48 - CRITICAL - Parsnp requires 2 or more genomes to run, exiting

bkille commented 2 months ago

Hi @yissachar17!

Just to clarify, you're using the same command and same version as you had previously? If that is the case, could you try outputting to a fresh directory (i.e. -o parsnpFiles-test)?

It shouldn't be the case that existing files in the output directory are messing with your run, but that's the only thing I can think of if nothing else has changed between runs...

Another possibility is the use of spaces and parenthesis in the reference filename. I just tried and was able to run Parsnp w/ -r "sequence (1).fasta", but bash wouldn't allow me to run it with -r sequence\ (1).fasta.

yissachar17 commented 2 months ago

Hi @bkille, thanks for getting back to me.

I managed to resolve the issue.

The issue seemed to be that I was running the parsnp command from a shared directory (with Windows). When I ran parsnp from a non shared directory, it worked!

bkille commented 2 months ago

Awesome! Thanks for keeping me posted and feel free to let me know if you run into any other issues.