Error: Line 1 of .ped file has more tokens than expected

[Ana Marija]

Hello,

I am trying to convert ped/map file into vcf file via:

module load plink/1.90

module load vcftools

plink --ped finalEDIC.chr1.pedc --map finalEDIC.chr1.map --recode vcf --out finalEDIC.chr1

But I am getting this error:
Rescanning .ped file... 0%
Error: Line 1 of .ped file has more tokens than expected.

format of .ped file is shown in attachment.

Is there is other way to convert .ped/.map to .vcf or there is something wrong with this .ped format?

Thanks

Ana

[Christopher Chang]

There appear to be two issues here.

1. .ped files are normally assumed to contain 6, not 5, columns before the genotypes begin.  The .ped in your screenshot appears to be missing the phenotype (6th) column.

2. However, plink complained about seeing more, not fewer, tokens than expected in the line.  This implies a mismatch with the .map file: each .ped line is supposed to have 2n + 6 columns, where n is the number of lines in the .map file.  If the missing phenotype column was the only problem, there would be 2n + 5 columns, which would be fewer than the expected 2n + 6.

[Ana Marija]

Hi,

thank you so much for your replay. This is what I have:

number of columns in .ped:
$ awk '{print NF}' finalEDIC.chr1.ped | sort -nu | tail -n 1
78175

number of lines in .map file:
$ wc -l  finalEDIC.chr1.map
39085 finalEDIC.chr1.map

so n=39085

number of columns in .ped =2n + 6=78176

Do you know what I can do about this?

Thanks

Ana

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[Christopher Chang]

Okay, looks like the second part of my previous message was incorrect, your lines do have exactly 2n + 5 tokens.  (There was an oversight in the .ped-validation code which caused an inappropriate error message to be printed here; this will be corrected in the next build.)  In this case, you should be able to use the --no-pheno flag to import this nonstandard .ped.

On Thursday, November 22, 2018 at 11:03:26 AM UTC+8, Ana Marija wrote:

Hi,

thank you so much for your replay. This is what I have:

number of columns in .ped:
$ awk '{print NF}' finalEDIC.chr1.ped | sort -nu | tail -n 1
78175

number of lines in .map file:
$ wc -l  finalEDIC.chr1.map
39085 finalEDIC.chr1.map

so n=39085

number of columns in .ped =2n + 6=78176

Do you know what I can do about this?

Thanks

Ana

On Wed, Nov 21, 2018 at 8:32 PM Christopher Chang wrote:

There appear to be two issues here.

1. .ped files are normally assumed to contain 6, not 5, columns before the genotypes begin.  The .ped in your screenshot appears to be missing the phenotype (6th) column.

2. However, plink complained about seeing more, not fewer, tokens than expected in the line.  This implies a mismatch with the .map file: each .ped line is supposed to have 2n + 6 columns, where n is the number of lines in the .map file.  If the missing phenotype column was the only problem, there would be 2n + 5 columns, which would be fewer than the expected 2n + 6.

On Thursday, November 22, 2018 at 5:53:46 AM UTC+8, Ana Marija wrote:

Hello,

I am trying to convert ped/map file into vcf file via:

module load plink/1.90

module load vcftools

plink --ped finalEDIC.chr1.pedc --map finalEDIC.chr1.map --recode vcf --out finalEDIC.chr1

But I am getting this error:
Rescanning .ped file... 0%
Error: Line 1 of .ped file has more tokens than expected.

format of .ped file is shown in attachment.

Is there is other way to convert .ped/.map to .vcf or there is something wrong with this .ped format?

Thanks

Ana

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[Ana Marija]

Hi,

thanks again, so where I would put that flag?

Maybe like this?

plink --ped --no-pheno finalEDIC.chr1.pedc --map finalEDIC.chr1.map --recode vcf --out finalEDIC.chr1

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[Christopher Chang]

Switch the order of the filename and the --no-pheno flag.

To understand why this is necessary, it may be useful to rewrite the corrected command line as follows:

plink \

  --ped finalEDIC.chr1.pedc \

  --no-pheno \

  --map finalEDIC.chr1.map \

  --recode vcf \

  --out finalEDIC.chr1

(Ending a line with '\' lets you split a command across several lines in most shells.)

On Friday, November 23, 2018 at 10:32:56 AM UTC+8, Ana Marija wrote:

Hi,

thanks again, so where I would put that flag?

Maybe like this?

plink --ped --no-pheno finalEDIC.chr1.pedc --map finalEDIC.chr1.map --recode vcf --out finalEDIC.chr1

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[Ana Marija]

Hi,

I did run it as you suggested:

plink --ped finalEDIC.chr1.ped --no-pheno --map finalEDIC.chr1.map --recode vcf --out finalEDIC.chr1

but I got again:

128952 MB RAM detected; reserving 64476 MB for main workspace.
Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.

Rescanning .ped file... 0%
Error: Line 1 of .ped file has more tokens than expected.

Any suggestion would be appreciated.

Thanks

Ana

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[Christopher Chang]

I’d need to look at your .map file and the first line of your .ped to investigate this further.

[Ana Marija]

Hi,

my .map file is in attach

and

my .ped file first line extracted is in attach as well.

Thank you so much for looking into this!

On Sat, Nov 24, 2018 at 6:40 PM Christopher Chang <chrch...@gmail.com> wrote:

I’d need to look at your .map file and the first line of your .ped to investigate this further.

[Christopher Chang]

Okay, the problem is that there are 34 blank lines scattered within the .map file; you'll need to investigate why they're there.

[Ana Marija]

HI Christopher,

I made my .map file like this:

awk '   BEGIN { while ((getline <"bed_chr_22.bed") > 0) {REC[$4]=$0}}
    {print REC[$2]}' < finalEDIC.chr22.dat > out22
awk '{$2=$6=""; print $0}' out22 | awk '{ print $1 " " $3 " " $4 " " $2}' >tmp22
sed "s/chr/ /g" tmp22 > finalEDIC.chr22.map

I can see there is 7 empty lines in this file:

grep -cvE '\S' finalEDIC.chr22.map
7

and zero empty lines in finalEDIC.chr22.dat and bed_chr_22.bed.

In attach I em sending you how .dat and .bed files look like.

Do you know maybe why I might have this problem?

Thanks

Ana

On Sun, Nov 25, 2018 at 10:35 PM Christopher Chang <chrch...@gmail.com> wrote:

Okay, the problem is that there are 34 blank lines scattered within the .map file; you'll need to investigate why they're there.

[Ana Marija]

Hi Christopher,

I cleaned (turned all in space separated) .bed file with perl::
perl -p -i -e 's/\t/ /g’ test.bed

then I created .map file again:
awk '   BEGIN { while ((getline <"test.bed") > 0) {REC[$4]=$0}}
    {print REC[$2]}' < test.chr1.dat > out1
awk '{$2=$6=""; print $0}' out1 | awk 'BEGIN {OFS = " "}{ print $1,$3,$4,$2}' >tmp1
sed "s/chr/ /g" tmp1 > test.chr1.map
sed -i 's/^ *//' test.chr1.map

but test.chr1.map has again 34 empty lines.

I printed those empty lines and they are these
awk '(NF==0){print NR}' test.chr1.map
1955
2119
3431
4027
4777
4880
5648
8364
11562
13020
13735
14168
14988
17249
17914
20560
20888
21056
21504
24523
24623
24627
26025
26571
30692
31565
31620
33049
33738
33752
35166
36376
37621
37876

and it seems those 34 empty lines are already happening in file out1 after this awk command:
awk '   BEGIN { while ((getline <"test.bed") > 0) {REC[$4]=$0}}
    {print REC[$2]}' < test.chr1.dat > out1

test.chr1.dat always has 2 columns and zero empty lines. and also test.bed has zero empty lines and always has 6 columns.

I will look into this further but please let me know if any other ideas are for this.

Thanks
Ana

[Ruth Waineina]

Hello,

I am facing the same problem of getting an error  that line 1 of .ped file has more tokens than expected.

kindly requesting for help

[Waqas Khan]

.ped file 

ERROR:
Problem with line 1 in [ C:\Users\Shadow\Desktop\plink-1.07-dos\snp.ped ]
Expecting 6 + 2 * 5 = 16 columns, but found more

.map file

Can anyone answer why I am getting this error, it is supposed to be executed, Please just look for data I have ped and map file format but when I run it o n the plink it gives me an error.

[Waqas Khan]

Thanks got the solution it was my data and the SNPs difference in .ped file

[Zuxi Cui]

Correct me if I’m wrong. It seems you have 5 SNPs in the map file.

However, you have more than 5*2=10 columns of nucleotides in the ped.

Terry 

Sent from my iPad

On Apr 1, 2023, at 22:34, Waqas Khan <waqaskh...@gmail.com> wrote:

.ped file 

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[Waqas Khan]

You were right about the data in. Ped file 

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