Comments (6)
Hi, thanks for your interest in nextNEOpi
@1 You can find more information in the supplemental material of our publication https://doi.org/10.1093/bioinformatics/btab759
@2 In the Class_II
directory you should not find MHC_Class_I
related/named files, because it is only for MHC_Class_II
results.
from nextneopi.
Oh sorry, I copy pasted the file name from class I but I meant this file (classII):
sample1_MHC_Class_II_all_epitopes_ccf_ref_match.tsv
There is only a fusion folder in it.
from nextneopi.
Can you attach the .nextflow.log
file, so that I can check?
from nextneopi.
Attached.
from nextneopi.
It seems that you did not specify the path to your local HLA-HD installation.
Your slurm-20852100.out.log
, which bwt is not the .nextflow.log
, shows:
WARN: WARNING: HLAHD not available - can not predict Class II neoepitopes
Here is the relevant section from the README.md:
Optional but recommended: Due to license restrictions you may also need to download and install HLA-HD by your own, and set the installation path in conf/params.config. If HLA-HD is not available Class II neoepitopes will NOT be predicted
Unfortunately we are not allowed to bundle and distribute HLA-HD, therefore nextNEOpi
users need to install it manually on their system if they want to also predict Class II neoepitopes.
HTH, closing this ticket for now
from nextneopi.
Thank you.
Reza
from nextneopi.
Related Issues (20)
- Bwa terminated with an error exit status (137) -- Execution is retried HOT 5
- Nextflow installation error HOT 3
- error message when run a test case HOT 12
- Error executing process > 'gatherMutect2VCFs (sample2)' HOT 11
- Target regions bed file for TESLA patients 4,8,9 HOT 3
- NeoFuse: long running time HOT 4
- pVACSeq chmod error HOT 4
- Process `installVEPcache (installVEPcache)` terminated with an error exit status (104) HOT 4
- nextNEO resources bundle installation issues HOT 4
- Failed to run, issues related to pvacseq , etc HOT 5
- Error executing process > 'pVACseq (sample1)' HOT 4
- including SNV/indel calling on RNA-seq data HOT 1
- HLA-HD silently fails if bowtie2 is not installed/loaded HOT 1
- Error executing process "installVEPcache" HOT 7
- How could I improve this pipeline?
- mkfifo: cannot create fifo : Operation not supported HOT 2
- `pVACseq ` terminated with an error exit status (1) HOT 2
- Process `get_vhla (test)` terminated with an error exit status (1) HOT 32
- amino acids sometimes doesn't match the reference or variant HOT 2
- Is .cram input format supported? HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from nextneopi.