Comments (5)
Hi @matthdsm, @chapmanb, @naumenko-sa,
I'm getting the same truncated files as @matthdsm, but only for GRCh37 and hg38, while hg19 completed successfully.
Looking at the ggd recipes, hg19 uses wget
to fetch the gnomad VCFs (gnomad_exome and gnomad_genome), while GRCh37 and hg38 both use the URL directly as an argument to vt decompose
.
I've tried rerunning the GRCh37 and hg38 recipes three times now, and they always fail at roughly (but not exactly) the same spot - leaving me with a ~400Mb gnomad_exome.vcf.gz
file and a ~340Mb gnomad_genome.vcf.gz
file.
For reference, here are the sizes of the hg19 version of these two files:
gnomad_exome.vcf.gz: 5391108579 bytes
gnomad_genome.vcf.gz: 26405145616 bytes
-- Paulo
from cloudbiolinux.
Hi Matthias @matthdsm and Paulo @pfpjs !
Thanks for reporting the issue and pointing out how to fix it!
I indeed see the same effect on my system.
I pushed a fix in my fork https://github.com/naumenko-sa/cloudbiolinux
and created a pull request for Brad @chapmanb.
Please let me know if this resolved the issue!
Sergey
from cloudbiolinux.
Thanks Sergey -- this got pulled and is available now. Thank you all for testing and reporting and let us know if you hit any other problems.
from cloudbiolinux.
Hi guys,
I was doing some digging and turns out we're making things too hard on ourselves. The annotation works just as well without decomposing/normalizing the gnomad vcf. What are your opinions on this?
Cheers
M
from cloudbiolinux.
Hi @naumenko-sa,
GRCh37 gnomad_exome.vcf.gz
completed sucessfully, thank you!
However, gnomad_genome.vcf.gz
also needs the wget "treatment". Thanks!
from cloudbiolinux.
Related Issues (20)
- Error while adding reference to the given genome to the base index file HOT 1
- Failed to install due to broken link HOT 5
- Feature request: Update Drosophila genome build to support dm6 HOT 5
- mirbase GFF file not installed for mmu even if it is present HOT 2
- a peculiar bug in grch37 dbnsftp recipe HOT 3
- gnomad_exome ggb randomly fails on chr1 HOT 5
- UNPACK_DIR: unbound variable HOT 3
- Issues with installing dbscSNV HOT 7
- bismark_indices.loc missing HOT 2
- Problems with centralized conda installation HOT 2
- Broad FTP login error is causing bcbio-nextgen data upgrade to fail HOT 7
- Integrate additional GiaB samples for validation HOT 1
- limit conda environments HOT 1
- tar -p option causes quota issues in case quota are enforced on group level HOT 3
- Don't use both mamba and conda to install packages
- Incorrect Ensembl release version for hg38 transcripts.yaml
- Installation problem conda package libtiff HOT 1
- Please submit cloudbiolinux/BCBIO related issues to bcbio github
- cloubiolinux.org website is hijacked or domain expired
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 cloudbiolinux.