phenotype file

aclay
Guest

phenotype file Nov 11, 2014 18:42:55 GMT

Quote

Post by aclay on Nov 11, 2014 18:42:55 GMT

Hi I am having issues with my phenotype file.
The error is
"Error: no individual is in common in the input files."
I have the file in the correct format: FID,IID (no header), .txt, NA's for missing...
Suggestions?
Thank you in advanced for your help.

see below:
Analysis started: Tue Nov 11 13:40:18 2014

Options:
--reml
--grm BCTOX5
--pheno gcta.s0221.pheno.2.txt
--prevalence 0.11
--covar gcta.s0221.covar.txt
--qcovar gcta.s0221.qcovar.txt
--out s0221_tox_phenotype
--thread-num 10

Note: the program will be running on 10 threads.

Reading IDs of the GRM from [BCTOX5.grm.id].
1269 IDs read from [BCTOX5.grm.id].
Reading the GRM from [BCTOX5.grm.bin].
Reading the number of SNPs for the GRM from [BCTOX5.grm.N.bin].
Pairwise genetic relationships between 1269 individuals are included from [BCTOX5.grm.bin].
Reading phenotypes from [gcta.s0221.pheno.2.txt].
There are 20302 traits specified in the file [gcta.s0221.pheno.2.txt].
The 1th trait is included for analysis.
Non-missing phenotypes of 0 individuals are included from [gcta.s0221.pheno.2.txt].
Reading quantitative covariates from [gcta.s0221.qcovar.txt].
4 quantitative covariate(s) of 1269 individuals read from [gcta.s0221.qcovar.txt].
Reading discrete covariate(s) from [gcta.s0221.covar.txt].
1 discrete covariate(s) of 1269 individuals are included from [gcta.s0221.covar.txt].

Error: no individual is in common in the input files.

aclay Guest	phenotype file Nov 11, 2014 19:26:04 GMT Quote Select Post Deselect Post Link to Post Back to Top Post by aclay on Nov 11, 2014 19:26:04 GMT I figured out the answer to my own question. This error had to do with a format issue brought forth by textwrangler software. Thank you for your time.

davejones
New Member

Posts: 2

phenotype file Jan 4, 2017 4:35:43 GMT

Quote

Post by davejones on Jan 4, 2017 4:35:43 GMT

Hi there aclay,
A few years on, but I was wondering if you had any additional information on the textwrangler error you encountered when using GCTA. I am having the exact same problem with my input pheno file.
Best,
Dave

i.e.
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.02
* (C) 2010 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* GNU General Public License, v2
* Queensland Institute of Medical Research
*******************************************************************
Analysis started: Wed Jan 04 14:32:20 2017

Options:
--reml
--grm Pmax
--pheno Pmax_Indiv.phen
--out Pmax_Indiv

Reading IDs of the genetic relationship matrix (GRM) from [Pmax.grm.id].
1048 IDs read from [Pmax.grm.id].
Reading the GRM from [Pmax.grm.gz].
Pairwise genetic relationships between 1048 individuals are included from [Pmax.grm.gz].
Reading phenotypes from [Pmax_Indiv.phen].
There are 11 traits specified in the file [Pmax_Indiv.phen].
The 1th trait is included for analysis.
Nonmissing phenotypes of 368 individuals are included from [Pmax_Indiv.phen].

Error: no individual is in common in the input files.

Jian Yang Administrator Posts: 362	phenotype file Jan 10, 2017 4:16:51 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by Jian Yang on Jan 10, 2017 4:16:51 GMT You might use the latest version of GCTA. It's very likely to be an issue of the IDs not being consistent between the files.

davejones New Member Posts: 2	phenotype file Jan 16, 2017 6:26:35 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by davejones on Jan 16, 2017 6:26:35 GMT Thanks Jian, Turns out that it recognises the pair of familyID and individualID. I had a different notation in my familyIDs within my phen file. Best, Dave

xnr94
New Member

Posts: 4

phenotype file Nov 3, 2021 15:08:48 GMT

Quote

Post by xnr94 on Nov 3, 2021 15:08:48 GMT

Hi there... I'm having the same issue. The funny thing is that the problem occurs in two different data sets.

In the first dataset, some covariate files work but others do not, and they were made in the same way, using excel and then generating a text document.

In the second dataset, I am trying to estimate genetic correlations by incorporating covariates within the same dataset. Below is an example of how I am incorporating these covariates.

1.- Family from bed file. There are 5 populations. Here I'm only showing the header rows.

0 2010010416A20A5E 0 0 0 -9

0 2010010416A20B3A 0 0 0 -9

0 2010010416A20B9C 0 0 0 -9

0 2010010416A20BDB 0 0 0 -9

0 2010010416A20C6A 0 0 0 -9

0 2010010416A20C8D 0 0 0 -9

0 2010010416A20CC2 0 0 0 -9

0 2010010416A20D1A 0 0 0 -9

0 2010010416A20DE8 0 0 0 -9

2.- Phenotype measured

0 2010010416AF0056 0 NA NA NA NA

0 2010010416AF639D 0 NA NA NA NA

0 2010010416AF6ABE 0 NA NA NA NA

0 2010010416ABCA90 0 NA NA NA NA

0 2010010416AF03B3 0 NA NA NA NA

0 2010010416AF8930 0 NA NA NA NA

0 2010010416AFB6EB 0 NA NA NA NA

0 201001041663B81E 0 NA NA NA NA

0 2010010416ABDB7A 0 NA NA NA NA

0 2010010416AF1800 0 NA NA NA NA
....
0 2018011533A9EDBE NA NA NA NA 1

0 2018011533A9E1A1 NA NA NA NA 1

0 2018011533A9E99E NA NA NA NA 1

0 2018011533A9EBAC NA NA NA NA 1

0 2018011533A9EB17 NA NA NA NA 1

0 2018011533A9EB74 NA NA NA NA 1

0 2018011533A9E1DC NA NA NA NA 1

When I try 1 with 2, 1 with 4, 1 with 5 it works. 2 with 3, 2 with 5 and 4 with 5 work. However when running 1 with 3, or 3 with 4, the program stops for "Segmentation fault (Core dumped)".

I am not sure if it is because of the number of samples since pop5 has the least number of samples and they all work with that one (1140 samples in total).

The rest have at least 1300 samples each. I have tested on my university server and on gcta installed on my personal notebook and still get the same error with the same populations.

Does anyone have any idea what could be happening?

jfreeman New Member Posts: 1	phenotype file Feb 3, 2022 17:52:48 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by jfreeman on Feb 3, 2022 17:52:48 GMT I ran into this same problem. I opened up my .fam file in a text editor (wordpad) and saw that my the iid in my .fam file didn't match the iid in the phenotype file. Once I fixed that problem, I was able to do all of my analyses.

Post by aclay on Nov 11, 2014 18:42:55 GMT

Post by aclay on Nov 11, 2014 19:26:04 GMT

Post by davejones on Jan 4, 2017 4:35:43 GMT

Post by Jian Yang on Jan 10, 2017 4:16:51 GMT

Post by davejones on Jan 16, 2017 6:26:35 GMT

Post by xnr94 on Nov 3, 2021 15:08:48 GMT

Post by jfreeman on Feb 3, 2022 17:52:48 GMT