Tobias Baril
Tobias Baril
Regarding the failures with RepeatModeler and RepeatMasker - can you successfully run these programs on these genomes in isolation? If so, it could be an issue with the random seed...
Okay great, it would be good to know if the RM runs complete successfully outside of the pipeline. An alternative might also be to increase the minimum # of sequences...
Hi @estolle, some of the solutions suggested in #145 might help for these strange genomes. A combination of reducing the # of iterations (for most genomes, 5 rounds with `-i`...
closing due to lack of activity. Please open a new issue if further assistance is needed.
Hi, Thanks for checking out Earl Grey! The `bc` command is only used for calculating the runtime of the pipeline, and is only invoked following the completion of an Earl...
Is it just the landscapes that are missing? I think the issue is this line: ``` Starting calculations WARNING. chromosome (NC_052526.2) was not found in the FASTA file. Skipping. Finished...
Closing due to lack of activity, feel free to reopen if needed.
Hi, thanks for checking out Earl Grey! Hmm, the fasta index looks okay and there aren't any strange invisible characters on that line. @jamesdgalbraith any idea whether this is linked...
A fix for this has been pushed in `v4.4.5` thanks to @jamesdgalbraith! This was linked to multiple instances trying to create the same index file during the divergence calculation. The...
Hi, In this case it looks like your system is killing the process for some reason (sig 9 is a kill signal from the kernel). This step is running a...