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Hi I was wondering if you have a fix for the following issue. I get this error:
```
0:00:14.95 Mapping 4.R1.fished.fastq to NUC reference...
0:00:22.52 Mapping 4.R2.fished.fastq to NUC referenc…
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Sorry, I am curious to know which parameter must be set in the project.yam in order to run phylowgs and bubble tree?
thanks!
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Running this command on the master node
```
./nextflow run nmdp-bioinformatics/flow-Optitype \
--with-docker nmdpbioinformatics/flow-OptiType \
--outfile hli-optitype.csv \
--bamdir s3://bucke…
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Hi
I am trying to use OptiType and get the error:
Error loading 'pyutilib.component' entry points: 'type object 'PluginGlobals' has no attribute 'push_env''
Traceback (most recent call last):
…
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Trying with @armish's setup (since mine didn't work; see https://github.com/hammerlab/biokepi/issues/418), I get some of these, which I believe are issues with OptiType itself:
```
### Kube-Job 5a…
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Hello,
I am using OptiType with Python 2.7.10. After installing some modules, I could run the analysis:
python /OptiType/OptiTypePipeline.py -d -v -i $curDir/NeoEpitopePrediction/${Tumor}_1.fastq …
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I ran tumor variant calling using an ensemble caller with vep annotation + hla calling for normal. I successfully obtained an annotated ensemble vcf, but the expected .csv containing optitype output …
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@tavinathanson discovered this during his recent trials. Here is the error log of an attempt to run OptiType on a legit data set:
```
Traceback (most recent call last):
File "", line 114, in
…
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With Pyomo 5.x the following error occurs for GLPK
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Hi,
I have a bcbio installed with GRCH37. Now that I have a client who is intersted in mm10. I was trying to do python bcbio_nextgen.py upgrade --genomes mm10 and I ran into Import Error for single…