repeatSubMatrix_setLogProb

[nkono]

Hi,

During the execution, it goes up to 4%, but then stops with the following message.
Command:
$ marginPolish minimap2.sorted.bam asm.fasta ./params/allParams.np.json -o output -t 32

Message:
[repeatSubMatrix_setLogProb] base 'Nn' not supported for repeat estimation

The draft genome is in multi-fasta format and does not contain any characters other than ATGC.
Is there any solution to this problem?

Thank you.

[tpesout]

Hi nkono, this repository is largely unmaintained but when I have some time I will try to take a look at your issue. Can you give me a brief description of what you're trying to do? It will also be helpful if you can run this again with the following command and upload the resulting log file:
marginPolish minimap2.sorted.bam asm.fasta ./params/allParams.np.json -o output -t 32 -a info 2>&1 | tee output.log

[nkono]

I created a bam file with long-read mapped to asm.fasta, and sorted/indexed (minimap2.sorted.bam)
Using this minimap2.sorted.bam file, I would like to polish the asm.fasta.
output.log

[tpesout]

Thanks @nkono, if there are reads which have non-standard characters then that might cause this problem also. Can you try these two commands to verify that all your data is composed of ACGTacgt?

cat asm.fasta | grep -v "^>" | grep -e "[^ACTGactg]"
cat minimap2.sorted.bam  | cut -f10 | grep -e "[^ACTGactg]"