Comments (16)
I have not seen this type of error before.
Just want to know more about the system.
Can you please paste the outputs of uname -a
and lsb_release -a
?
Can you check the memory limit on your torque system?
from rvtests.
It's the Dutch LISA system on the SurfSara cluster:
https://userinfo.surfsara.nl/systems/lisa/description
uname -a
Linux login2.lisa.surfsara.nl 3.2.0-4-amd64 #1 SMP Debian 3.2.88-1 x86_64 GNU/Linux
lsb_release -a
LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:core-4.1-amd64:core-4.1-noarch:security-4.0-amd64:security-4.0-noarch:security-4.1-amd64:security-4.1-noarch
Distributor ID: Debian
Description: Debian GNU/Linux 7.11 (wheezy)
Release: 7.11
Codename: wheezy
I'm afraid I don't know what a torque system is. For the kinship-command I requested a node with 64 GB RAM (QPI 8.00 GT/s), which would also have a 20 MB cache.
Also, given that it occured with the smaller subcohort but not the larger one, I doubt it is a memory issue.
from rvtests.
from rvtests.
Do you mind attached the first 5 lines of the input VCF and PED file?
How many lines does the PED file have?
Just want to make sure the input file look all right. Thanks.
from rvtests.
Thanks for the suggestion. I am trying to run kinship with a single thread right now, but it may be a couple of hours before the job is processed by the cluster.
The ped file and VCF are attached to this post. I removed the sample IDs from the VCF, and edited those in the PED file for the sake of anonimization, but that shouldn't be a problem. The PED file contains 32 lines in total (a header line and 341 samples).
EDITED: data files removed. As they are no longer relevant.
from rvtests.
The single-thread analysis (using the chromosome 22 file rather than the combined genome file) gave the same output. The only difference that I could see was that the "strol: invalid argument" message repeated 76 times.
Effective Options
--inVcf chr22.imputed.poly.vcf.gz
--out kinship_matrix_CC
--xHemi
--xLabel X
--ped dataF_P90c_TRAILS_CC_anthro.txt
--bn
--minMAF 0.05
--thread 1
[INFO] Program version: 20170210
[INFO] Analysis started at: Fri Jun 9 16:55:30 2017
[INFO] Empiricial kinship will be calculated.
strtol: Invalid argument
[INFO] Start creating empirical kinship from VCF file.
[INFO] Using default maximum missing rate = 0.05
terminate called after throwing an instance of 'std::logic_error'
what(): basic_string::_M_construct null not valid
from rvtests.
from rvtests.
As I don't have clue as this moment, do you think the VCF can be invalid? Maybe you can run to check validity using this: https://github.com/zhanxw/checkVCF
from rvtests.
I think I found the problem. I discovered that I could run a kinship analysis if I replaced the phenotypes (but not the sample IDs) of the smaller subset with values taken from the larger subset.
Then I realized that there where missing gender values in the smaller subset. These unsexed samples are missing from my phenotype file. However, when I arbitrarily made them all females, the kinship analysis ran without error.
Does the gender value in the ped file affect the kinship analysis? Because if it doesn't, using arbitrary genders will have solved this problem.
from rvtests.
Thanks for the information.
Yes for the X-chromosome analysis, as vcf2kinship needs to account for gender and zygosity in the X non-PAR region.
Just to be clear, since the input is chromosome 22, the results should be the same with or without the gender information.
from rvtests.
OK. I am going to rerun the kinship analysis with the old, unmodified phenotype file while using the peopleExclude argument to ignore these samples. That should hopefully avoid the problem.
from rvtests.
Does this file chrALL.imputed.poly.vcf.gz
include both autosomes and sex chromosome?
from rvtests.
Yes, it includes chromosome X.
I tried generating a kinship matrix while excluding the unsexed samples. It worked, but it gets a bit strange, since I did get 36 "strtol: Invalid argument" warnings in the console output. When I did not exclude the unsexed samples, but set them all to female, I did not get any warnings. (For this test, I also used the chr22 vcf file as input, rather than the chrALL file, in order to save space, so this wasn't a comprehensive test.)
I still don't get what the warning means. If I were to give an arbitrary gender to these 76 samples, and then exclude them via the peopleExclude argument, would that affect the kinship matrix? Since these 76 samples have no phenotypes, they are not going to be used in the analysis anyway.
from rvtests.
Adding this for clarity: when I generated a kinship matrix where the unsexed samples had been set to female, I used the chrALL file. However, I am running another analysis that is taking up a lot of disk space, so when I tried generating a kinship matrix while excluding the unsexed samples, I only used chr22. I don't think that explains the error messages, but I wanted to add it for completeness.
from rvtests.
You can safely ignore the warning "strtol: Invalid argument". It is just verbose warning messages when RVTESTS tries to convert a non-numeric value. For example, when RVTESTS process "NA", it will give this warning. I realize that this warning is no longer necessary. The latest version thus stops displaying warnings.
from rvtests.
Excellent. The issue has been resolved, then. Thank you for your help!
from rvtests.
Related Issues (20)
- User-specified weight per variant
- SKATO: rvtest frozen/stalled (3 variants) (minimal example provided) HOT 1
- What do the duplicated lines in burden test with covariates output mean ?
- Instructions to build without all of the third parties ? HOT 5
- What/where is --outputRaw collapsed genotype?
- Reference allele output from rvtest
- Rvtests SKAT,SKATO keeps on running after removing one gene from '--gene' list
- No variants found in gene
- Some permutated p-values >1
- Incorrect phenotype file format [ m2_pheno.pheno ], check column number
- SKAT/CMC: Missing covariates are not imputed, but dropped HOT 2
- Runtime Bug Chromosome 2 UKB WES
- Output MAC or MAF for SKAT-O kernel test
- Output explanation
- Segmentaion fault - rvtests using RStudio Workbench HOT 1
- NAs in assoc file
- Order of Operations when using Frequency filter and Sample exclusion.
- Segmentation fault while running --meta cov
- --setFile how are overlapping regions handled?
- exactCMC N00 is less than N10 and N01 < N11
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 rvtests.