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

[valery-shap]

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]

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.