bbuchfink/diamond

Use custom score matrix error?

liufuyan2016 opened this issue · 1 comments

Dear,
I use custom score matrix below :
image
and running the below command use diamond v2.1.9.163 :
diamond blastp --more-sensitive -d dataset.fa -q query.part_001.fa -p 5 -f 6 qseqid sseqid pident length mismatch ppos gapopen qstart qend sstart send evalue bitscore qlen slen stitle -o dataset.fa.1.blast.out --max-target-seqs 5 --custom-matrix matrix.txt --gapopen 11 --gapextend 1
There are one error:

#CPU threads: 5
Error: The ALP library failed to compute the statistical parameters for this matrix. It may help to adjust the gap penalty settings.

How to solve it? How to set the --gapopen and --gapextend parameter?
Thank you very much!
I am looking forwards your reply!

I'm not familiar with the internals of the ALP library and why it may fail for certain matrices.