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It seems like `compute_f_from_AA_graph` function in the amplicon classifier part of the pipeline might have something up with it as it is consistently throwing the following error:
```
home/bkw21…
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Hi,
Thanks for developing this great tool. Would it be possible to add an argument to AmpliconArchitect to force it to use a specific set of SV breakpoints? I know there's an option to include the…
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Set this up over the weekend and thought I'd list the software dependencies that I required which weren't explicitly mentioned in the readme:
scipy, numpy, python 2, pysam, mosek, matplotlib.
In add…
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### Description of the bug
Hi - first time nextflow and circdna user. I am trying to run circdna on a tumor BAM file that has already been processed. I followed the instructions in the README and enc…
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### Description of the bug
The AmpliconArchitect related processes use this structure to set an environment variable:
`export AA_DATA_REPO=${params.aa_data_repo}`
without staging the files in that …
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https://mp.weixin.qq.com/s/PqZWZ1e_vK5AuY1XIgUD3g
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Hi,
Thanks for making this software available to the community.
I've done several rounds of AA (using different seed intervals) and it usually runs successfully.
In a recent run, some of the sa…
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Hi! When I run prepareAA it can't find mt reference genome (GRCh38.tar). The first error I got was:
Traceback (most recent call last):
File "PrepareAA.py", line 505, in
ref = gdir + refFnam…
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Hello,
I am running AmpliconSuite-pipeline and I got results successfully from most of the input bam files. However, in this particular bam input, I got this error:
##########
"Wrote 005-32_cnvki…
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### Description of the bug
When using circdna with AmpliconArchitect for a already aligned BAM file, i ran into the following problem:
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Acces…