Comments (8)
from ibdkin.
Hi Victor,
Thanks for reaching.
Based on your situation, I will try to add option "--part 10 1" to your command. If the problem is still there, I will check the input files.
Best,
Ying
from ibdkin.
Thank for your answer!
I double checked the inputs and they look ok. For values like --part 10, 20, or 50 the result is the same even when I increase the memory availability (700G). Just for one chr that I had a different error : Error!, maker ranges for chromosome do not cover the position 21138926
Even when my data have that region
Any thoughts?
from ibdkin.
Hi Victor, I don't think this is a memory problem.
Did you check the range file? it should cover all your markers.
And also check the chromosome identifier, it should be in the same codes for all input files.
If the range file is good, I will cehck 1) ibd file, compare the format with the example to look difference. 2) for each IBD segment, the end position should be larger than the start position. 3) the genetic map, both the physical and genetic positions should be in increasing order.
Best,
Ying
from ibdkin.
Hi Ying,
I found that there was something wrong during the compression of the files and now is working
Thank you so much for your time!
from ibdkin.
Hi Ying,
After checking all my files and running again I have found this error:
Error!, maker ranges for chromosome do not cover the position 4160868
What it means exactly? Do I have to modify my range sfile?
from ibdkin.
from ibdkin.
Hi @YingZhou001,
It has been a while since we met via Zoom in the MCMC workshop this summer :).
Victor and I are from the same group. We looked at this issue together this afternoon. We figured that the issue was caused by the memory overflow from str1
or str2
to chr
.
IBDkin/src-v2.8.7.7/parallel.c
Lines 623 to 625 in 61ccecb
IBDkin/src-v2.8.7.7/parallel.c
Lines 634 to 636 in 61ccecb
It would not be an issue if the sample names are short. But we happened to have long sample names in our IBD input files (as long as 58 bytes, longer than buffer size (BUFF1 or 32) .
Lines 16 to 17 in 61ccecb
After we edited #define BUFF1 32
to #define BUFF1 128
, #define BUFF 128
to #define BUFF 512
and recompiled the code, it runs without crashing immediately. Hope it runs smoothly to the end. @vicbp1
from ibdkin.
Related Issues (6)
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 ibdkin.