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On Langley:
```python
>>> import gotoh2
>>> handle = open('gisaid-aligned.fa')
>>> fasta = gotoh2.convert_fasta(handle)
>>> len(fasta)
19371
>>> fd = dict(fasta)
>>> seq = fd["hCoV-19/USA/MI-M…
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In `debug/Autobot.log`
```
Error in update_alignment: length of sequence hCoV-19/England/NOTT-11152A/2020|EPI_ISL_457576|2020-05-01 does not match reference.
```
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@ewong347 are you still triggering downloads manually? otherwise the `covizu.sh` script should be running the whole analysis to update the JSON files.
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Will have to identify internal nodes via landmark tip labels..
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We submitted 40 sequences that passed SIGNAL metrics, but 15 were rejected due to frameshifts. We should add this level of reporting/QC to ensure sequences are ready for GISAID.
> Your submission B…
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See notes on how to benchmark assemblers here:
[200503_rce_assembler_benchmark_notes.pdf](https://github.com/ababaian/serratus/blob/master/notebook/200503_rce_assembler_benchmark_notes.pdf)
Anyo…
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Hi,
Thanks for the great tool!
I assume that for integration with the UCSC genomes browser that the `global_assignments.pb` and/or `global_samples.vcf` files are regularly updated. Is it possibl…
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I can run bbbq_2 only **on a part of** the proteome locally, due to memory errors. Get it to run on Peregrine by allocating enough memory.
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**Current Behavior**
Hello, I am encountering an error when running your default build with my GISAID sequences on Job 6: Refining Tree. The job can't be finished because it returns a "ValueError:…
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add this https://github.com/hCoV-2019/pangolin