Can not access local variable 'read_mems_tmp' when using --use_NAM_seeds about ultra HOT 2 CLOSED

Hi @ksahlin

Thank you for your reply, yes indeed the prolem was with the zcat command.

from ultra.

Hi @FadelBerakdar ,

First off, I will make it easy for me and say that the StrobeMap version (--use_nams) is experimental.

However, I had a quick look at what you pasted and, from the command lines, it looks like you have only 900 reads calling it with slaMEM, and 0 reads(?!) in the --use_nam run. Have you verified the input read file is not empty or malformatted?

Maybe the <(zcat ...../ENCLB632GYO_1k.fastq.gz) is causing some trouble not unpacking all the reads in time for mapping as you are streaming in the reads. I don't think the fastq parser can parse a stream or gzipped input unfortunately.

I had plans over the coming days revise a bit in the seed finding part of uLTRA (slaMEM/StrobeMap) at that time I can have a look into parsing gzipped formats as well.

from ultra.