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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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Why snp file produced by syri is empty and followed by error #190

Closed InfiniteLaugh closed 1 year ago

InfiniteLaugh commented 1 year ago

Hello, I tried to run syri to obtain SV, SNP, Indel, etc., All SV files seem normal, but the program dropped out at the SNP step, leading to an empty file. The input file alignment coordinates file was obtained from mummer4, using the code as follows:

nucmer --prefix qry ref.fa qry.fa -t 10 -l 50 -c 100 --maxmatch
delta-filter -i 90 -l 100 -m qry.delta  > qry.i90_l100_m.filter.delta
show-coords -THrd qry.i90_l100_m.filter.delta > qry.i90_l100_m.filter.THrd.coords

But error occurs at the step of SNP, I am wondering if I should replace parameter -m with -1, is this the reason for this issue? Snipaste_2023-04-18_00-53-24

mnshgl0110 commented 1 year ago

The error implies that show-snps (from mummer) could not be run correctly. Please check that show-snps is in the bash working environment. Alternatively, try using the -s parameter of syri to parse the path to show-snps.