Parsnp - Error: problem reading files from ./genomes (multifasta input)

[rmartischang]

Hi,

I am running parsnp v1.2 from Ubuntu (using WSL2), to align one annotated isolate (.gbk) with 84 strains in multifasta format. Thus, the resulting command is:

parsnp -g Genomes_Ecoli_LOEX.FASTA/reference/contigs_MR1_annotated.gbk -m Genomes_Ecoli_LOEX.FASTA/genomes/*.fasta -c

-g because it is an annotated strain
-m because of the multifasta format
-c to force each strain of the folder as an input

And I got an error as a result. "problem reading files from ./genomes.."
Do you know if there's an error in the command ? or maybe it is due to the version used ?

Warning: Cannot determine OS, defaulting to linux |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest *************************************************************************** SETTINGS: |-refgenome: Genomes_Ecoli_LOEX.FASTA/reference/contigs_MR1_annotated.gbk.fna |-aligner: libMUSCLE |-seqdir: ./genomes |-outdir: /home/rmartischang/bioinformatic/P_2021_04_08_164000507664 |-OS: linux |-threads: 32 *************************************************************************** <> -->Reading Genome (asm, fasta) files from ./genomes.. ERROR: problem reading files from ./genomes

Many thanks

[bkille]

Hi @rmartischang, thanks for using parsnp!

The regular expression syntax you are using to pass the input fasta files is a feature of parsnp v1.5+ and is not available in 1.2. You can try instead running

parsnp -g Genomes_Ecoli_LOEX.FASTA/reference/contigs_MR1_annotated.gbk -m Genomes_Ecoli_LOEX.FASTA/genomes/ -c

if the Genomes_Ecoli_LOEX.FASTA/genomes/ directory only contains fasta files. However, we'd recommend you upgrade to version 1.5 as there are some additional bugfixes and 1.2 is no longer supported.

Thanks again and hope this helps!

-Bryce