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When
* running the in-mem mode
* with the standard max memory limit
* and a dataset with a long cobs matching (plasmids)
it seems to me that too few cobs instances are being run in parallel, l…
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Coming off of #11, I expanded the database 10x to see if I could create any collisions by accident. I did this by introducing 1 SNP ten different times per allele. I also kept the original allele. …
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Validate whether there are any allelic collisions with md5 (or other?) on the Salmonella chewbbaca.online database.
* hashsum each allele from chewbbaca.online and put it into a table with original…
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HQ+LQ xz batches compression ratio is 4.4% (lower is better, this is the compressed size over uncompressed size ratio):
```
/hps/nobackup/iqbal/leandro/cobs/compress_all_data/mof-compress/661k_compr…
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**Description**
Hello @rpetit3 ,
We are currently using the `shigeifinder` wf in the bactopia tools, but it stucks for many hours. Please find the logs below.
> (base) gilmansiu3@gilmansiu3-Z49…
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**Description**
After running `bactopia download --build-all envtype conda`, I get an error that the environment cannot be solved.
**Steps to Reproduce**
Steps to reproduce the behavior:
```
(b…
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After during benchmarking, several processes stalled (see https://github.com/karel-brinda/mof-search/issues/83), I'm getting the following errors after re-running the pipeline:
```
$ make match
s…
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This could substantially improve the COBS part.
I think we already have everything for this:
1. COBS is fixed and tested with the memory mode
2. We already have a mechanism to reduce the sum of i…
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貼吧活動：(請查閱 [SARS-CoV-2 Timeline by 2020.02.21](https://github.com/agorahub/_meta/blob/agoran/theagora/sari/Memorandum_2020-02-21_SARS-CoV-2-Timeline_Nathan.pdf?raw=true), by Nathan :cloud: )
- Colla…
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# Bactopia v3
I am making progress towards a version 3 release of Bactopia (🥳). This version of Bactopia is going to introduce some fun an exciting things, but at the same time its going to break …