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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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Time for converting from .ggr to <multi-fasta alignment output (concatenated LCBs)> #105

Open valery-shap opened 2 years ago

valery-shap commented 2 years ago

Hello,

I'd like to have a file where I can identify the snps with the gene and I tried the command: harvesttools -i parsnp.ggr -M msa_lcb.aln and it stucked on writing the output. then I tried harvesttools -x parsnp.xmfa -M msa_lcb.aln and it stucked too. there is no error. converting to -S worked for some minutes. What is the normal time for coverting to alignment file with concatenated LCBs? Upd It has taken hours for converting on hpc server (88 cpus and 250 gb memory). But I have another question. Where I could find the information about coordinates of lcb (start and end) in the alignment file?

Valery

bkille commented 10 months ago

Hi @valery-shap,

How large is the xmfa file? The coordinates of the LCB are in the header of each record within the LCB. The header has the following format

[fileIndex]:[i]-[j] [strand] cluster[clusterIndex] s[contigIndex]:p[contigPosition]

i.e. the corresponding location of the sequence in the file fileIndex is the contigIndexth contig in the file and starts at position contigPosition.