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Dear, I use custom score matrix below : 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!
The text was updated successfully, but these errors were encountered:
I'm not familiar with the internals of the ALP library and why it may fail for certain matrices.
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Dear,
![image](https://private-user-images.githubusercontent.com/23466455/329768739-ca051b7e-a607-45a1-bbf2-9e4e76f6b09e.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.SLMgAhnYavIF7XStZ7TRc-6MTU3n16OcbjBz_pDjQjE)
I use custom score matrix below :
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!
The text was updated successfully, but these errors were encountered: