Error: No valid entries in --score file.

[V Lagou]

Hi,

I am using the following command:
R --file=/mypath/PRSice_v1.25/PRSice_v1.25.R -q --args \
plink  /mypath/PRSice_v1.25/plink_1.9_linux_160914 \
base /SNPTEST_output/SNPTEST_trait1_PRS_noduplo.out \
multiple.base.phenotypes T \
base.phenotypes.names trait2 \
target chunkALL.chrCHRNUM.phased.impute2_filtered_score_noduplo \
geno.as.list T \
slower 0 \
sinc 0.01 \
supper 0.5 \
binary.target F \
covary T \
user.covariate.file /Imputation_output/covar_file_PRS.txt \
covariates sex \
remove.mhc T \
clump.snps T \
multiple.target.phenotypes T \
pheno.file /Imputation_output/pheno_file_PRS.txt \
target.phenotypes inv_norm_trait2,inv_norm_trait1 \
target.phenotypes.binary F,F

In the *PROFILES.log files that are generated, I get the following error:
For example for 1PROFILES.log:

PLINK v1.90b2i 64-bit (8 Sep 2014)
11 arguments: --bfile flipped_target_1 --noweb --out 1PROFILES --q-score-range rangelist.txt rangelist_ranges --score rawfile.raw --silent
Hostname: r3i0n15
Working directory: /Imputation_output
Start time: Mon Jun 26 21:16:27 2017

Note: --noweb has no effect since no web check is implemented yet.
Random number seed: 1498504587
64386 MB RAM detected; reserving 32193 MB for main workspace.
734923 variants loaded from .bim file.
703 people (291 males, 412 females) loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Calculating allele frequencies... done.
Total genotyping rate is 0.99903.
734923 variants and 703 people pass filters and QC.
Note: No phenotypes present.
Error: No valid entries in --score file.

Any ideas why this might be? Thanks very much in advance.

[V Lagou]

and here it is the general log file:

Using data on multiple phenotypes for target data
Constructing Polygenic Scores for  trait2  Risk
 #################################
 #
 #  Check options match
 #
 #################################
[1] "Using current directory as working directory"
 #################################
 #
 #  Check base input format
 #
 #################################
[1] "WARNING: No CHR column in base data"
[1] "WARNING: No BP column in base data"
[1] "WARNING: No A2 column in base data"
[1] "NB: READING BETA NOT ODDS RATIO"
[1] "WARNING: No SE column in base data"
 #################################
 #
 #   Remove Ambiguous SNPs
 #
 #################################
 #################################
 #
 #   Clump
 #
 #################################
 #################################
 #
 #   Deal with strand flips if target is in genotype format and produce input files for polygenic scoring
 #
 #################################
 #################################
 #
 #   Polygenic scoring!
 #
 #################################
 #################################
 #
 #   Regression Models
 #
 #################################
Polygenic Scores Regressed on  inv_norm_trait2  Status

[Sam Choi]

Hi, are you running multi-base file PRSice? Because you've specified multiple.base.phenotype T but we only see one base file

On top of that, could you maybe show 1-2 line of the rawfile.raw  so that we can see if that's of the correct format (this should be generated from the base file by PRSice, if your base file is of correct format, then this should in general be in a correct format)?

[V Lagou]

Hi Sam,

Thanks for your response. I modified lines 3-5 of my command to be able to run the multi-base PRSice. Are they correct now?
base SNPTEST_PHEN.NAME_PRS_noduplo.out \
multiple.base.phenotypes T \
base.phenotypes.names trait1,trait2 \

I can see two raw files in my folder and here it is how they look like:

==> rawfile.raw <==
10:100188454 C -0.0124346
10:100226367 C -0.0981006
10:100305887 A -0.597043
10:100426796 A -0.133898
10:100469054 A 0.317647
10:100480823 A 0.255751
10:10075364 G -0.150078
10:10075460 A 0.0767561
10:100824365 T 0.302153
10:100860954 T -0.201694

==> temp.raw <==
10:10001753 T 0.0679049
10:10001794 G 0.0281846
10:10001801 T 0.039734
10:10001829 G 0.0152702
10:100023489 C -0.137593
10:100025125 <CN0> 0.133292
10:100025128 C 0.0240529

I also get the following error:
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
Execution halted

[Sam Choi]

Yup, your command is now correct. Could you please show me the full log by also including plink.silent F debug.mode T in your command? (the main reason is that there are a lot of read.table function call in PRSice and it is difficult to pin point it without the full log)

Thanks

[V Lagou]

Hi Sam,

Please find attached the two log files. I hope we can identify the problem in those.

[V Lagou]

Hi Sam,

Apologies for the multiple emails. Did you have the chance to look at my log files?If we cannot resolve this, I will need to find a different way of calculating polygenic risk scores, so I would really appreciate your advice.

Best regards,
Vaso

[Sam Choi]

Based on the error message, it seems like PLINK cannot read the .raw files for the score construction, which is strange. Maybe you can try performing the analysis on 1 base trait and one target trait first and see if that works? 

[V Lagou]

Unfortunately didn't work.

Could you please confirm that my input files have the correct format? Based on the error I get, the score file has no valid entries.

>head rangelist.txt
-0.01 0 -0.01
0.00 0 0.00
0.01 0 0.01
0.02 0 0.02
0.03 0 0.03
0.04 0 0.04
0.05 0 0.05
0.06 0 0.06
0.07 0 0.07
0.08 0 0.08
 >head rangelist_ranges
10:100188454 0.894362
10:100226367 0.595994
10:100305887 0.0473174
10:100426796 0.495065
10:100469054 0.394544
10:100480823 0.163102
10:10075364 0.399717
10:10075460 0.515284
10:100824365 0.142554
10:100860954 0.543205
>head rawfile.raw

[Laura Ibáñez]

Hi Sam, 

I am having the very same error: Error: No valid entries in --score file

I am using the following code: PRSice 

base AllStroke_Mantra_PRScise.txt 

target PRScise_Mantra_Plink

pheno.file All_Delta.txt 

binary.target F 

allow.no.sex T 

covary T 

user.covariate.file All_Delta_Covariates.txt 

covariates Sex,Age,Baseline,PC1,PC2 

fastscore T barchart.levels 0.00000005,0.000005,0.00001,0.001,0.01,0.05,0.2,0.5,1 quantiles T 

figname AllStroke_Mantra_Delta

Following this post I used the debug mode, but my guess is the porblem is with plink since the PROFILE file is not generated.

Any suggestion on why is this happening?

Thanks a lot

Laura 

[Sam Choi]

In that case, it might be worth while to also use the 

plink.silent T 

parameter which should let us know about the error encountered by plink.

Alternatively, we now have PRSice 2.0 under beta testing and should have a better error report system in place. maybe you can try it out here

[Laura Ibáñez]

Hi, 

just in case it is useful to anyone, I found what the problem was. The allels in the base file were coded in lower case whereas in the plink file is coses in upper case. I was a simple problem, but it has taken me a while to realise.

Hope this can help somebody.

Lau