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It seems that hydrogen-, butyrate-, acetate-, and lactate-producing microbes are annotated from the same source (Barcenilla_2000), but they have different frequency/confidence_interval values. Maybe t…
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### Week 1 - Get to know the community
- [X] Join the communication channels
- [X] Open a GitHub issue (this one!)
- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
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[We've provided Graphnet with contracts for all the tables we expect to use in the CIPHA study](https://github.com/opensafely-core/databuilder/issues/485), except for the Second Generation Surveillanc…
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**Description**
Attempting to pipeline ONT reads (using a single specified reference)
but bactopia: QC_reads fails
executor > local (27)
[cf/a28af4] process > BACTOPIA:GATHER_SAMPLES (E20544…
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Hi there,
I recently did some whole genome sequencing and tried out bactopia to assemble my genome. I followed the instructions on the page and ran into this error below. I am not sure why the pro…
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Hello,
I am using conda to install AMR++ pipeline but the demo crashed while parsing nextflow.config with the following error:
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ nextflow run main_A…
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**Description**
Hi, I have tried multiple times to run the bactopia staph aureus tutorial in a docker container and am getting this java error and it is failing at the QC step. Do you have any sugg…
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Hi
I have this error while running.
Please, help me with that.
I have macbook pro.
WARN: Task runtime metrics are not reported when using macOS without a container engine
[61/f69571] NO…
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**Description**
When I specific "--adapters db/adapters.fa", pipeline failed.
```bash
executor > local (3) …
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Hi,
I can not use MLST search in --species "Escherichia" because of the bug in bactopia datasets update as following:
Thanks!
Haitao
(bactopia-dev) lh@ubuntu:~$ bactopia datasets -…