Comments (2)
This is a known limitation -- it's hard to fix without significant investment in a backend we don't want to maintain forever. This issue generally pops up when people use tables instead of matrix tables to process wide files. Can you rewrite the GTEx processing script to use import_matrix_table instead of import_table, then process as a matrix?
from hail.
@tpoterba yes I think that's what we'll do when we come back to this, thanks
from hail.
Related Issues (20)
- [fs] Document and expose the AsyncFS interface
- [vds] update gnomAD's public HGDP+1kG sparse matrix table to be a VDS
- [query] investigate larger Zstd buffer sizes
- [query] read_movie_lens can sometimes fail
- [batch] Submitting a Batch using the hailtop.batch library may raise "Cannot enter into task" errors HOT 5
- [query] In Query-on-Batch, the calculation for IBD is incorrect HOT 1
- [query] `n_partitions()` after `read_matrix_table(..., _n_partitions=...)` produces one fewer partitions than expected
- [chore] Host Grant Chau's browser in a manner similar to ukbb-rg HOT 1
- [query] importing single cell data: add skip_n_rows in import_table and a filename field HOT 7
- [query] QoB should profile continuously in real-time, not just at the end of a job
- [query] VDS combiner will not load a successfully completed plan causing combiner to be rerun when a successful run has been completed HOT 2
- [query] Hail must run large-scale tests before a release
- [hailctl] hailctl dataproc connect on windows doesn't work
- [hailctl] hailctl on windows uses a non-writable data dir HOT 1
- [query] ipython 1.18.1 (and possibly other versions) does not work with query on batch HOT 1
- Error in parsing vcf files to hail ("cannot set missing field for required type +PFloat64") HOT 1
- [batch] "gsa" keys in azure can expire and are never updated
- [query] investigate GRCh38 patch versions and determine if we need to be versioning our Loci by patch
- [fs] drop support for hail-az
- [auth] In Azure, service principal secrets and the oauth2 secret must be automatically rotated
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 hail.