Detecting exogenous viral sequences

[NabilAsyraf98]

Hi there!

Thanks for writing this tool!

I am trying to detect retroviral sequences in a human ONT long-read data. But it was stuck at "Identifying simple repeats' at the first batch.

For the custom library -lib option, I simply merged several viral genomes into a fasta file with the following header format

This is the command ran: RepeatMasker -lib ~/LYMPHOMA/viral_genomes/viral_sequences/combined_viral.fna -xsmall -gff -s ~/LYMPHOMA/Z4739_files/Z4739_genome.fa

I wonder if RepeatMasker can detect exogenous viral sequences in long read data? or do I have to modify the sequence headers in the custom library?

Thanks !!!

[rmhubley]

I don't see an obvious issue with that. I wonder if you would mind sharing the two sequence files from this search ( library and genome ) so that I might try to and reproduce this.

[NabilAsyraf98]

Hi, the two sequence files are too huge to share here - 2 GB and 124 GB. I ran on a HPC node with 20 cpus and 60 gb of RAM.

[rmhubley]

I assume the genome is 124GB file. If so, can you try breaking up the genome the genome into batches and try running a smaller input with the same library? For example since the strange behaviour begins with the first internally-generated batch, you could try taking the first 1MB of the genome file and run that. You might be able to reproduce the problem with a much smaller sequence.