kim-fehl

Produce pycoQC's read length non-interactive plot in log scale too

1

### Description of bug In interactive plots mode, MultiQC v.1.11 aggregates pycoQC's Nanopore read length distributions and produces the plot in log scale which is very convenient. However, in `--flat`...

search progress bar is still running when using --quiet option

1

### Description of bug Neither `-q` or `--quiet` option does not hide this part of log: ``` /// MultiQC 🔍 | v1.11 | multiqc | MultiQC Version v1.12 now available!...

sambamba --version's output doubled

1

``` $ sambamba --version sambamba 0.8.2 by Artem Tarasov and Pjotr Prins (C) 2012-2021 LDC 1.27.1 / DMD v2.097.2 / LLVM11.0.0 / bootstrap LDC - the LLVM D compiler (1.27.1)...

Now if you run into any problem with Flye (in my case it was absent `python2.7` which is neither checked in `configure` script nor stated in the prerequisites) and restart...

Otherwise pipeline fails at certain stage (several numactl issues are already opened, python2.7 is required for Flye step in hybrid assembly pipeline)

Invalid segment Error when building reference of the rat genome

3

I'm using `kb ref` command from [kallisto-bustools package](https://www.kallistobus.tools/kb_usage/kb_ref/) and RefSeq genome [mRatBN7.2](https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/) of _Rattus norvegicus_. Here is the command: `kb ref -i mRATBN7.cdna.idx -g mRATBN7.t2g -f1 mRATBN7.cdna.fna ~/genomes/GCF_015227675.2_mRatBN7.2_genomic.fna ~/genomes/GCF_015227675.2_mRatBN7.2_genomic.gtf` The...

Seemingly unnessecary warning about 'missing' escaped wildcard reference

1

 Warning: Cannot find reference 'sample' in 'Rule 'load_illumina_reads' wildcards'

Show a warning if special fasta headers format is violated

2

In a large dataset of automatically downloaded sequences there can be names including "|" symbol. I concatenate class and train/test labels also automatically. So, when I try to analyze this...

Skip 'splitting the reference genome sequence' stage if it has already been split

1

Seems that this stage could be skipped if already done during previous runs, especially considering that it is using only one CPU and is somewhat slow. `Splitting the reference genome...

Initially I tried to feed just assemblies' fasta files (just two of 5.5 mb), not gbk annotations into the program, and that led to uncontrolled RAM consumption. Probably user need...