Timothy Rhyker Ranallo-Benavidez

GetCountersForRead requires random access mode

5

Hello, I have a dataset where the KMC database is 1.4 Terabytes. I have been using the GetCountersForRead function, but as currently implemented this requires the database be loaded in...

Recover missing alignment

1

Hello, I am wondering how I can recover an alignment that exists when mapping to a reference with a single sequence, but which does not exist when mapping to a...

Multisample Calling with BND (translocation) variants

1

Hello, I am running into an issue with multisample calling for BND variants. I am merging two samples together. Both of the following lines are in the multisample vcf, even...

munmap_chunk(): invalid pointer on ubam file - KMC crashes on BAM with long reads

4

Hello, I am running the following KMC command: ``` kmc -k31 -t42 -m50 -sm -ci1 -cs100000000 -fbam data.u.bam data tmp ``` and I receive the following error at the end...

Run stages separately

3

Hello, I was wondering if it is possible to run stage 1 and stage 2 separately? The reason why I am asking is that I am trying to optimize how...

Hello, It is not a pressing issue but I just wanted you to be aware that KMC currently doesn't compile with Python 3.11. I receive the following error: ``` py_kmc_api/libs/pybind11/include/pybind11/pybind11.h:2026:52:...

Hello, Would it be possible to use BAM files as input? Thanks for any insights.

Snakemake 8 compatibility

2

Hello, I recently updated my version of Snakemake to version 8, and now Verkko doesn't work. Specifically, I get the following error: ``` snakemake: error: unrecognized arguments: --reason ``` According...

Hello, I get the following error when I try to run the flagger pipeline. ``` [2024-05-03 07:30:55,44] [error] BackgroundConfigAsyncJobExecutionActor [ddf63c0arunSecPhase.secphase:NA:1]: Error attempting to Execute java.lang.Exception: Failed command instantiation at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:674)...

Error when cleaning up metadata when using workdir in snakefile

2

Hello, When I run a dryrun in snakemake, I get the following error: ``` IncompleteFilesException: The files below seem to be incomplete. If you are sure that certain files are...