Timothy Rhyker Ranallo-Benavidez issues

Results 14 issues of


                                            Timothy Rhyker Ranallo-Benavidez

Running Snakemake --touch gives PulpSolverError

**Snakemake version** I have snakemake 8.20.6. **Describe the bug** When I run "snakemake BLPt0001/assembly/verkko/assembly.haplotype1.fasta --touch --cores 1" I get a PulpSolverError. **Logs** ``` Traceback (most recent call last): File "/tgen_labs/barthel/software/miniforge3/envs/snakemake/lib/python3.11/site-packages/snakemake/cli.py",...

bug

Skip kmers with N instead of skipping entire sequences with N

Hello, Currently Reindeer will skip any queried sequence with Ns. However, I was wondering if would instead be possible to only skip any kmers with Ns (or actually, to output...

Output contains only * with no counts

Hello, I created a Reindeer index on the T2T genome, and then queried the genome against the index in order to get the counts of all the kmers. The commands...

Error during index step, terminate called after throwing an instance of 'std::invalid_argument'

Hello, I ran the following command: Reindeer --index -f fof_unitigs.txt -o /scratch/rranallo-benavidez/bcalm/quick_out2 -t 42 This was the output: ``` ############# REINDEER version 1.4.6 ############# Command line was: /REINDEER/Reindeer --index -f...