Shellfishgene

Add search_pcr function

2

It would be nice if vsearch could search for PCR products given primer sequences, as the usearch `-search_pcr` function does. The `search_oligodb` command probably does the heavy lifting and would...

GeneMark `make_nt_freq_mat.pl` fails because of empty files

4

Hi! My Braker run fails at the GeneMark-EP stage with the error below. I think the cause is that all the files in `GeneMark-EP/run/EP_ini/` are emtpy (`acc.seq, don.seq, intron.len, parse.ep_ini`)....

Sometimes the last line on the screen in a comment thread is show as partly garbled text:   This is resolved as the comment is scrolled further up.

Feature request: Remove unfixable reads

4

Hi! It would be nice to have an option to remove unfixable reads (and their pairs) from the output.

GARD fails due to MPI setup (?)

7

Hi! I just tried to run the pipeline with profile local and singularity, with the test data `bats_mx1_small.fasta`. However GARD fails, apparently due some MPI setup stuff. I'm not sure...

Hi! The first checkM step that defines the root dir does not work when using Singularity as those containers are read only, and that command tries to change a config...

Singularity container does not work due to read only filesystem

1

Hi! I tried the Singularity container, but get below error, Probably whatever that is should be extracted to a tempdir outside the container. Conda works for me. ``` singularity run...

EXCEPTION: error opening file: tmp/s2228.fq ()

8

I tried to run ORNA on a large dataset (each fastq file ~45 GB, paired end), but it fails with the above error. The DSK step seems to work fine,...

Hi! I would like to try ORP on our cluster, but we only have singularity available. I converted the Docker image, and it works to some extent. However using ```singularity...

Pulseaudio 100% CPU

10

Hi! I'm currently running birdnet-go on a Debian VM under Proxmox. Nothing apart from birdnet-go is running or installed. After a week or so the CPU goes to 100% usage...