Rachel Colquhoun comments

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                                            Rachel Colquhoun

run_indep_wkflow_with_gnu_par hangs after parallel build step before combine

Yes please

problem with run_indep_wkflow_with_gnu_par.pl

This was the thing with the memory I think. Check the build log in one of the sample directories and see if it says it ran out of memory From:...

Is `find_mean_covg' still appropriate in estimate parameters?

Rediscovered why had this method of overriding neg bin model: ``` found mean 30.6201 found variance 30.8196 p: 0.993528 and r: 4700.38 Tue May 14 11:21:21 2019 Collect kmer probability...

Make genotype compatible issue with long alleles

I think it can happen like you describe. Although I would have thought that the updated genotype for record1 would be '.' not '0' (as we don't know about the...

Update est_abundance.py

It turns out my kraken report had the columns switched because of an incorrect merge. This change would safeguard against bad file merges like mine, but isn't strictly necessary

Should `min_kmer_covg` be per sample in `pandora compare`?

yes

Cigar format using ssw

Thanks! I'll try the python decode function you suggest

Stop producing empty alleles

So the issue here is to do with multiple levels of nesting which can make it really hard to "get the previous letter and add to both". E.g. suppose that...

Confusuing option in seq2path

Not read the thread, but I think this was useful for development of mixture genotyping, not so useful for other people. Sent from my Samsung Galaxy smartphone. -------- Original message...

Differences in gene presence/absence

This doesn't look like a simple bug to me, and as you say is likely some combination of parameter/algorithm effects. Worth noting that I have got some built in overrides...