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I copied test data from example_data folder provided by the neoflow.
the input_vcf_list.txt file looks like:
```
experiment sample file file_type
crc_test sample1 /neoantigen2/inpu…
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Hi, I’m encountering errors while running pvactools (version 4.4.1) on a SLURM-managed HPC cluster. The pipeline fails during MHC Class I predictions, specifically with NetMHCcons and MHCflurry. Below…
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Run the example data, I receive this error:
python NeoPredPipe.py -I /mnt/bwa-0.7.17/wes/gatk4/gatk-4.0.6.0/0809_somatic.vcf -H /mnt/bwa-0.7.17/output/arcasHLA/arcasHLA/HLA/HRR572954.genotype.json …
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Hi,
I am attempting to use antigen garnish to predict neoantigens from fusion proteins predicted by arriba/starfusion/fusioncatcher.
I took the predicted peptides from those programs (quite long, mi…
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Hi, I have been trying to run antigen garnish for a while with your testdata and now it seems to run fine with parallel and netMHC. The issue is that in the folder as e.g. ag_f236b988a09e438ea2 it doe…
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Hi,
I have run the NeoPredPipe.py as:
`python NeoPredPipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10`
INFO: Annovar reference files of build h…
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Hello, thanks for the fantastic tool!
I have been using it for many years, but I am facing a bug I have never encountered.
I am running Neopredpipe for a set of samples, separating them by SNPs an…
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Thanks for the tool! I'm using docker version of NeoPredPipe, but I met the same error as #17.
```
Traceback (most recent call last):
File "/software/NeoPredPipe-1.1/NeoPredPipe.py", line 523, …
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hi
The prediction step takes a very long time. Can the running speed be increased by increasing the number of cores?
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**Describe the bug**
When I run the example code:
```
if (is_mhcnuggets_installed()) {
peptides