Closed gunjanpandey closed 11 months ago
Unmasked repeats is the main problem.
Did you run RepeatModeler 2.0 to get a repeat library and then softmask your query with this library? Same for the reference genome.
Alternatively, try to reduce the chunksizes to get more but smaller jobs.
Thanks Michael,
I did not mask the genomes. I shall try again after masking. Could you please tell, if these steps are correct for preparing it for input in TOGA
Almost correct. After RepeatModeler 2.0, pls soft-mask both assemblies with RepeatMasker (we use rmblastn). Then produce the alignment chains. Then run TOGA.
https://github.com/hillerlab/make_lastz_chains/issues/10 to keep only one open performance-related issue
Could you please tell if something is wrong with this command as it is running even after 4 days. It started with running in a cluster occupying a total of around 500 single core jobs but around 125 jobs are still running.
make_chains.py --project_dir OUTPUT --executor slurm --cluster_parameters '-A AB-123456' --executor_partition defq --force_def chicken bird chicken.2bit bird.2bit