Carl Mathias Kobel

vcf_parse header fail

4

I just installed a fresh version of snippy on linux with conda, I get the following error in snps.log when I'm calling with reads: ``` ### bcftools view --include 'FMT/GT="1/1"...

I've been looking for a SNP-caller that does not depend on a reference genome. How hard would it be make snippy work on the core genome of a set of...

Nullarbor report without reads

3

Hello. We have become very excited about Nullarbor, and especially the report. I wondered if it would be somehow possible to the isolate set part of the pipeline. That is,...

Question about prefilling contigs

7

It is described in the documentation that one can reuse contigs across nullarbor runs by using the prefill option, such that {ID} is substituted with the ID of each sample....

database_handler.py:51: UserWarning: Database does not exist at path None

6

Hello I just installed DRAM with conda on a fresh miniconda3 install on two independent HPC's After running the ```DRAM-setup.py prepare_databases --output_dir DRAM_data``` step, I get the following error on...

-o option should have argument `required=True`

1

https://github.com/WrightonLabCSU/DRAM/blob/a5f225718c5ff312ec8ccaefbb61daaa12452705/scripts/DRAM.py#L35 Shouldn't the -o 'output' option be required? If I omit it an exception is thrown because the default -o parameter is NoneType ``` (DRAM) cmkobel@login-5 ~/userwork/dram $ DRAM.py annotate...

Wiki link to 404

1

Hello Thanks for maintaining DRAM In the [wiki under section 3a DRAM distill](https://github.com/WrightonLabCSU/DRAM/wiki/3a.-Running-DRAM#dram-distill) there is a link to an example https://shafferm.github.io/examples/dram/ But that link goes to a 404 page on...

Add Gapseq

3

Add gapseq ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a recipe, use "Add"...

Database update?

2

How old is the uniref database that CheckM2 is currently using? I see a reference to 3rd june 2018 in the main publication but am not sure if it has...

OSError: [Errno 30] Read-only file system

3

Hi I wish to [run](https://github.com/cmkobel/assemblycomparator2/blob/a05c7f5fa0d6fd8138aefdc876422897ef32e572/snakefile#L978) `checkm2 database` from apptainer in a large reproducible pipeline that automatically downloads necessary databases. Checkm2 is [installed with conda](https://github.com/cmkobel/assemblycomparator2/blob/master/conda_definitions/checkm2.yaml) inside the container. When i call...