Albert Vill

> My purpose is to compare all the sequences in all fasta files in this directory against each other and cluster them. Concatenate the individual files, then run cd-hit on...

Related issue: https://github.com/arq5x/bedtools2/issues/905 And a Biostars post with more context: https://www.biostars.org/p/9490546/

My workaround: https://www.biostars.org/p/9490546/#9493168

### Edit See [issue #78](https://github.com/linnabrown/run_dbcan/issues/78) ---- Hello @linnabrown. Sorry to resurrect this old issue. I'm having the same problems with run_dbcan v.2.0.11, installed via conda following your instructions. Here are...

> I also had the same problem here, and the cgc.out file came empty. Then I checked my protein sequences and made sure that each protein has the same name...

I've found the issue with run_dbcan 2.0.11. Adding the optional `-t all` parameter causes the program to break. Exclusion of `-t` results in the correct output using the provided test...

More context for the observed error can be found in issue #50 https://github.com/linnabrown/run_dbcan/issues/50#issuecomment-931522785

I came across this thread while trying to add bootstrap annotations onto the `RAxML_bestTree` file generated as part of the StrainPhlAn workflow. After specifying `-f a` to perform a rapid...

This is a post-hoc fix that doesn't address the problem with CRT, but I've implemented a `fix_repeats` option in my R-based minCED parser that appends spacer subsequences to repeats based...

I think the issue is that Biostrings does not consider terminal gaps in alignments to be indels. See https://github.com/Bioconductor/pwalign/issues/2. `ATCG` is retained if you specify `with.Lindels = FALSE`. ```r subject...