Dmitry Antipov

Colors not updated after new csv loaded

2

Seems that node colors taken from csv files are not updated after new csv loaded if they are not directly mentioned in the new csv file. For example, if I...

When running large swarm of jobs on NFS cluster sometimes I see that snakemake is waiting for files way more longer than it is stated in latency-wait option This is...

Was trying to use mashmap binary provided with mashmap3 release, and it seems that it is not dependence-free. Still require libgsl.so.25, libopenblas and, after fixing that, specific versions of stdlib...

meryl count assertion failed with large K

1

Tried to run with relatively large k (101), got this assertion ``` meryl count k=101 compress hifi.fasta.gz output 101.hpc.meryl Start counting with THREADED method. meryl: meryl/merylCountArray.C:512: uint64 merylCountArray::add(kmdata): Assertion `wordEnd

verkko does not always continue it's run correctly after crashes in hi-c

20

i.e. MissingInputException in rule alignBWA in file /data/antipovd2/devel/verkko/lib/verkko/Snakefiles/8-hicPipeline.sm, line 199: Missing input files for rule alignBWA: output: 8-hicPipeline/mapped002.bam wildcards: nnnn=002 affected files: 8-hicPipeline/split/hic2002.fasta.gz ERROR! Not running final consensus since no...

Better error reporting

1

Crashes are hard to find in current verkko log, also at some moment it would be nice to have more feedback like unoptimal parameters detected, or something went not how...

Hi-C plus Trio on same run

2

while hi-c jumping is not included we should not allow to use both hi-c and trio in the same run.

split coverage of a repetitive node to it's multiple copies. That may allow to simplify tangles better, distinguishing real low covered nodes from repeats.

Since the cutoff used for plasmid prediction differs to that one used in plasmidVerify, viralVerify outputs lots of plasmid sequences as unknown. Cutoff selection for plasmid prediction should be improved.