Patrick Bohn

cuDNN Runtime Error with RTX 3070, Pytorch 1.8.0a0, CUDA11.1, cuDNN 8.0.5

17

Hi Seymour, Thank you for the great work of bonito, it seems to quickly surpass the other basecallers. I am now trying to basecall some PCR amplicon data with it...

Nanopolish eventalign on direct RNA data fails when "--sample" flag is set

1

Running nanopolish eventalign on direct RNA data, basecalled with guppy 3.6.1 with parameters `--samples --print-read-names --scale-events` fails with the error `nanopolish: src/nanopolish_squiggle_read.cpp:1107: std::vector SquiggleRead::get_scaled_samples_for_event(size_t, size_t) const: Assertion `curr_sample_time >= (this->sample_start_time...

.tombo.index file ReadData object order is different than in documentation

2

Hello, I wanted to investigate the signal-matching-scores of my reads after resquiggling, and if I understand correctly this is most straightforward by looking into the tombo.index files (see quote below)....

Does Tombo plot kmer for RNA use reverse complement kmers?

1

Hi, I want to plot kmer values of direct RNA sequenced samples, and got it to work successfully, but it appears that C and U center bases have the lowest...

Documentation for tombo build_model estimate_alt_reference could be clearer

1

Hello, I have been trying to train an alternative model to get more accurate RNA mod detection at higher modification densities, and was trying to run `tombo build_model estimate_alt_reference ...`...

Attempting to push an image to sylabs returns fatal error decoding entity: invalid OjbectId in JSON: "username"

1

**Version of Singularity** What version of Singularity are you using? Run: ``` $ singularity --version singularity version 3.0.3-1 ``` **Describe the bug** Running on Windows in a vagrant VM, after...

Please add a notification that **no** conda environment should be active during the install. Having a conda environment with a newer version of numpy and python active during the install...

As mentioned in the title, when an error is raised via tombo_helper.error_message_and_exit() the sys.exit() call (see below) should return a non-zero value to ensure that errors are properly caught by...

Missing bam/cram file should return an error code

2

Hi, when running perbase base-depth with an incorrect BAM/CRAM path, even though stderr reports `thread '' panicked at 'Indexed BAM/CRAM: FileNotFound [...] perbase/src/lib/par_granges.rs:159:72`, it seems that no error code was...

[Request] An option to filter out signal spikes

5

Hi Hasindu, thank you for developing f5c and the detailed documentation with it, it is incredibly fast. I am using it to detect RNA modifications, and in one part of...