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Hey dear team,
I am experiencing memory issues in the creation and computation/optimization of large likelihood functions (that consist of a codon model, such as RELAX, and multiple alignments and …
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If I try:
```
anvi-self-test --suite pangenomics
````
I will get the following output. The error is at the bottom.
```
:: Output directory ...
/var/folders/86/v68d1x9s59128vx4pr1kl…
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Hello, I am attempting to run FEL for a batch of several genes on a cluster as the following lines:
inputRedirect = {};
inputRedirect["01"]="Universal"; // genetic code
inputRedirect["02"]="/added/…
CS-CH updated
5 years ago
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e.g. file ``msf/C_gen.msf`` on branch 3360 aka v3.36.0 which starts as follows:
```
$ head C_gen.msf
!!NA_MULTIPLE_ALIGNMENT
MSF: 4483 Type: N Apr 16, 2019 12:20 Check: 0 ..
Name: …
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one codon sequence can not be detected when it was inputted together with other 28 sequences.
The sequence is :
>QY6AD9.2
------------------------------------------------------------
------------…
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Trying to using your image at Dockerhub but I reach a point where mafft is called and it isn't part of the build.
(I'd also note that your build file doesn't seem to pull in the revbayes package as…
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simulatefastq-36 has riboviz/tools/create_fastq_examples.py which produces test data building up to Duncan & Mata-style:
* `data/simdata_UMI3_4nt.fastq` - 4nt UMI at 3' end
* `data/simdata_UMI5and…
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In one of your examples, you show that the alignment wraps after X characters, similar to what it does when you look at a clustal alignment written to file. That doesn't happen when I try to use it. H…
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Extend RiboViz to use [UMI-tools](https://umi-tools.readthedocs.io/en/latest/) (discussed in #37) for barcode and UMI extraction and subsequent deduplication.
* #57 is a precursor to this issue, re…
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Hi Klaus,
This issue relates to to the one I asked a while back (and it was closed by you).
I've decided to use simSeq() to generate sequences under different substation models.
To do this, I…