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plink2 giving multiple errors
plink2 --bfile fixed --pheno final_noheader.csv --covar covariates.txt --glm --out association_results
    PLINK v2.00a5.12LM AVX2 Intel (25 Jun 2024)    www.cog-genomics.org/plink/2.0/
    (C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3
    Logging to association_results.log.
    Options in effect:
      --bfile fixed
      --covar covariates.txt
      --glm
      --out association_results
      --pheno final_noheader.csv

    Start time: Tue Jul 30 15:58:13 2024
    31777 MiB RAM detected, ~21461 available; reserving 15888 MiB for main
    workspace.
    Using up to 16 threads (change this with --threads).
    45 samples (0 females, 0 males, 45 ambiguous; 45 founders) loaded from
    fixed.fam.
    638 variants loaded from fixed.bim.
    Error: No entries in final_noheader.csv correspond to loaded sample IDs.
    End time: Tue Jul 30 15:58:13 2024

So I'm finding traits with snp using plink and my snp data but it giving this error. What do I do?

plink2
• 1,099 views • link
updated by bk11 • bk11 • written by puneet • puneet

The error clearly says that there is not match between the samples IDs. I suggest to check the FID and IID in the respective first and second column of .fam files. They should correspondingly match with first and the second columns in your final_nonheader.csv file.

• 0 views • link
written by bk11 • bk11

so this is how my .fam look

 0  6008    0   0   0   -9
0   6039    0   0   0   -9
0   6042    0   0   0   -9
0   6188    0   0   0   -9
0   6243    0   0   0   -9
0   6919    0   0   0   -9
0   6924    0   0   0   -9
0   6926    0   0   0   -9
0   6932    0   0   0   -9
0   6951    0   0   0   -9
0   6958    0   0   0   -9
0   6959    0   0   0   -9
0   6961    0   0   0   -9
0   6967    0   0   0   -9
0   6989    0   0   0   -9
0   6992    0   0   0   -9
0   7000    0   0   0   -9
0   7064    0   0   0   -9
0   7092    0   0   0   -9
0   7094    0   0   0   -9
0   7143    0   0   0   -9
0   7147    0   0   0   -9
0   7158    0   0   0   -9
0   7163    0   0   0   -9
0   7186    0   0   0   -9
0   7199    0   0   0   -9
0   7231    0   0   0   -9
0   7244    0   0   0   -9
0   7255    0   0   0   -9
0   7296    0   0   0   -9
0   7424    0   0   0   -9
0   7460    0   0   0   -9
0   7520    0   0   0   -9
0   7521    0   0   0   -9
0   7525    0   0   0   -9
0   8214    0   0   0   -9
0   8236    0   0   0   -9
0   8239    0   0   0   -9
0   8241    0   0   0   -9
0   8326    0   0   0   -9
0   8354    0   0   0   -9
0   8365    0   0   0   -9
0   8387    0   0   0   -9
0   8420    0   0   0   -9
0   8424    0   0   0   -9

this is final_nonheader.csv

IID FID Phenotype
Cnt-1   7064    15.3
SLSP-30 2274    32.3
Rmx-A180    7525    33.2
Aa-0    7000    33.3
An-2    6996    35.8
HovDala-2   6039    36.1
Lip-0   8325    37
LAC-3   94  37.8
Ang-0   6992    37.8
Hi-0    8304    39.4
Ka-0    8314    39.5
EDe-1   7110    40
LAC-5   96  40
shahDara    6962    40.3
TOu-E-11    366 40.5
Kno-18  6928    40.5
Pu2-23  6951    40.6
Kas-2   8424    40.7
Se-0    6961    41
Ra-0    6958    41.3
Kin-0   6926    41.5
Gy-0    8214    41.8
MIB-22  173 42.2
MIB-28  178 43.1
Fei-0   8215    43.1
Dra-2   7105    43.3
Sq-8    6967    43.6
Rsch-4  8374    43.6
HR-5    6924    43.8
Ren-1   6959    44
LI-0F-095   641 44.2
Ta-0    8389    44.2
TOU-A1-116  282 44.7
Lp2-6   7521    44.9
KoIn    8239    45
Tou_A1-43   321 45.7
Petergof    7296    45.9
DraiV1-5    5887    46.1
LDV-34  126 46.5
LDV-25  116 46.5
MIB-84  223 46.7
Draiv1-14   5896    47.1
TOU-A1-96   357 47.7
Kelsterbach-4   8420    47.9
HSM 8236    48.1
DralV6-35   6005    48.8
PAR-4   259 48.8
DralV6-16   5987    49.1
Ga-0    6919    49.1
TDr-1   6188    49.2
Gr-1    8300    49.5
Go-0    7151    49.7
Lom1-1  6042    49.9
TOU-A1-62   328 50.3
Ste-3   2290    50.4
Gu-1    7150    50.7
GD-1    8296    50.8
MIB-15  166 51.1
Lz-0    6936    51.2
St-0    8387    51.3
TOU-I-17    378 51.3
Ct-1    6910    51.6
LC-0    8323    51.7
LDV-14  104 51.8
Liarum  8241    52.1
Ha-0    7163    52.3
Mnz-0   7244    52.5
Ga-2    7141    52.5
Rak-2   8365    52.6
TDr-3   6190    52.6
Lis-1   8326    53.2
Map-42  2057    53.5
Per-1   8354    53.6
Hey-1   7166    53.9
TOU-H-13    374 54.2
Gie-0   7147    54.3
Lm-2    8329    54.5
Tottarp-2   6243    54.5
Ge-1    7145    54.7
Fr-4    7135    54.8
Di-1    7098    55
Da-0    7094    55.1
Krot-2  7205    55.2
Duk 6008    55.5
Com-1   7092    56.1
JI-3    7424    56.4
Gr-5    7158    56.9
Mh-0    7255    57.3
ESt-0   7128    57.5
PAR-3   258 57.5
Da(1)-12    7460    57.5
Co-2    7078    57.8
N7  7449    58
Alst-1  6989    58.3
Sap-0   8378    58.5
Kro-0   7206    58.9
Lp2-2   7520    59.3
Ep-0    7123    60.3
Li-7    7231    61.3
Fi-1    7139    61.4
Kl_5    7199    61.9
Kelsterbach-2   7188    62.6
Gel-1   7143    63.6
Ler-1   6932    65.6
LDV-58  149 66.6
Kn-0    7186    68.3
Db-0    7100    68.9

so what changes i have to do...

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written by puneet • puneet

You should match the first column of .fam file with the first column of final_nonheader.csv file and the second column of .fam file with the second column of final_nonheader.csv file. You can do this in R or Unix which ever is suitable for you. Finally make sure that all the subjects in your .fam file are present in your final_nonheader.csv file.

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written by bk11 • bk11

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