Comments (5)
weizhouUMICH
commented on August 23, 2024
Hello,
Could you please share a more detailed log file. e.g. what is the format of the your dosage file?
Thanks,
Wei
from saige.
momo1210
commented on August 23, 2024
Hi Wei,
I just used your example file and example code and got the error message as below.
SPAGMMATtest(
+ vcfFile= "genotype_10markers.vcf.gz",
+ vcfFileIndex="genotype_10markers.vcf.gz.tbi",
+ vcfField="GT",
+ chrom=1,
+ minMAF=0.0001,
+ minMAC=5,
+ sampleFile="sampleIDindosage.txt",
+ GMMATmodelFile="example.rda",
+ varianceRatioFile="example.varianceRatio.txt",
+ SAIGEOutputFile="example.SAIGE.vcf.dosage.out.txt",
+ numLinesOutput=2,
+ IsOutputAFinCaseCtrl=TRUE,
+ )
1000 samples have been used to fit the glmm null model
obj.glmm.null$LOCO: FALSE
Leave-one-chromosome-out option is not applied
variance Ratio is 1
1000 sample IDs are found in sample file
[1] 1000 4
[1] "IID" "IndexInModel" "IndexDose.x" "IndexDose.y"
1000 samples were used in fitting the NULL glmm model and are found in sample file
minMAC: 5
minMAF: 1e-04
Minimum MAF of markers to be testd is 0.0025
Analysis started at 1537465735 Seconds
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Abort (core dumped)
Any idea about this?
I used SAIGE_0.29.3 version and fantasia as the server to run.
Thanks!
Min-Lee
…________________________________
From: weizhouUMICH <[email protected]>
Sent: Thursday, September 20, 2018 4:37:28 PM
To: weizhouUMICH/SAIGE
Cc: momo1210; Author
Subject: Re: [weizhouUMICH/SAIGE] step 2 unexpectedly terminate (#48)
CAUTION: This email originated outside the University of Michigan
DO NOT click links or open attachments if the sender is unknown to you.
Hello,
Could you please share a more detailed log file. e.g. what is the format of the your dosage file?
Thanks,
Wei
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#48 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ApUvMDcNwmibcP91v2J0k5mshOlIzMqwks5uc_yIgaJpZM4WrSl6>.
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
from saige.
weizhouUMICH
commented on August 23, 2024
Hi Min-Lee,
Thank you for letting me know about the error. A bug was found in the savvy library for reading vcf and sav dosages and has now been fixed. You may try the new version 0.29.4 on vcf files and please let me know if you have any other question.
Thanks,
Wei
from saige.
momo1210
commented on August 23, 2024
Wei, Thanks!
After re-install 0.29.4, I still got the same error message for step2.
library(SAIGE)
SPAGMMATtest(
- vcfFile= "genotype_10markers.vcf.gz",
- vcfFileIndex="genotype_10markers.vcf.gz.tbi",
- vcfField="GT",
- chrom=1,
- minMAF=0.0001,
- minMAC=5,
- sampleFile="sampleIDindosage.txt",
- GMMATmodelFile="example.rda",
- varianceRatioFile="example.varianceRatio.txt",
- SAIGEOutputFile="example.SAIGE.vcf.dosage.out.txt",
- numLinesOutput=2,
- IsOutputAFinCaseCtrl=TRUE,
- )
1000 samples have been used to fit the glmm null model
obj.glmm.null$LOCO: FALSE
Leave-one-chromosome-out option is not applied
variance Ratio is 1
1000 sample IDs are found in sample file
[1] 1000 4
[1] "IID" "IndexInModel" "IndexDose.x" "IndexDose.y"
1000 samples were used in fitting the NULL glmm model and are found in sample file
minMAC: 5
minMAF: 1e-04
Minimum MAF of markers to be testd is 0.0025
Analysis started at 1537563549 Seconds
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_M_create
Abort (core dumped)
Could you please check it again?
Thanks!
Min-Lee
from saige.
jinshaw16
commented on August 23, 2024
Dear Wei and Min-Lee,
I was running into similar problems but think I resolved it by putting the chromosome number in quotation marks e.g. chrom="1" rather than chrom=1.
Hopefully this resolves it for you, too.
Best wishes,
Jamie
from saige.
Related Issues (20)
- SAIGE-GENE+ install HOT 3
- Error in getopt(spec = spec, opt = args) : long flag "bedFile" is invalid HOT 4
- Error at step2 on chrX
- Can't install
- Can dominant model be used in single variant test?
- samples in geno file do not have phenotypes
- createSparseGRM error
- possible issue with categorical variables used as covariates?
- Should this SAIGE be closed since you have a new SAIGE page?
- How do you create the SparseSigmafile?
- createSparseGRM script (step0) doesn’t work
- Step1, sorting of sample ids
- Trying to get LOCO=True to work
- Error in mainRegionInCPP
- R CMD INSTALL SAIGE
- Chromosome coding UKBB
- Error running Step 1 on UKBB dataset.
- The appropriate sample size for continuous and binary traits analysis in SAIGE-GENE+
- Pre-computed group files for UKB WES
- Step 1 with sparse GRM gets stuck on "use sparse kinship to fit the model" 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 saige.