Beagle 5 error messages

[Victor Hsu]

Hello, 

I have plink file merged from (SNP 170K and 220K) map and per file.

I want to use Beagle 5 (beagle.27Jan18.7e1.jar).

I use vcf file by plink --recode vcf.

Then got the error when I was run the Beagle.

ERROR: REF field is not a sequence of A, C, T, G, or N characters at 1:81639936 [3]

ERROR: REF field is not a sequence of A, C, T, G, or N characters at 1:25209358 [3]

ERROR: REF field is not a sequence of A, C, T, G, or N characters at 1:72626728 [3]

ERROR: REF field is not a sequence of A, C, T, G, or N characters at 1:43201740 [1]

ERROR: REF field is not a sequence of A, C, T, G, or N characters at 1:110315014 [1]

So I add my plink command with --snp-only just acgt.

I try to open the vcf file. then genotype all become break end (./.)...

Anyway, I use the vcf to run Beagle again.

Then I got the

Exception in thread "main" java.lang.IllegalArgumentException: ERROR: missing REF or ALT allele at 0:211200

at vcf.BasicMarker.checkAlleles(BasicMarker.java:130)

at vcf.BasicMarker.extractAlleles(BasicMarker.java:312)

at vcf.BasicMarker.<init>(BasicMarker.java:249)

at vcf.VcfRecGTParser.<init>(VcfRecGTParser.java:70)

at vcf.BitSetGT.<init>(BitSetGT.java:74)

at vcf.VcfIt.lambda$static$7(VcfIt.java:90)

at vcf.VcfIt.lambda$new$8(VcfIt.java:192)

bala bala.......

I do the search, some people suggest the add maf=0 (but plink said mac must be >0)

So, I have no ideal what I can try? I also try to remove use -not-chr 0 x y mt combined with mac 0.05 and --snps-only

then I got

xception in thread "main" java.lang.IllegalArgumentException: ERROR: missing REF or ALT allele at 1:102143472

at vcf.BasicMarker.checkAlleles(BasicMarker.java:130)

at vcf.BasicMarker.extractAlleles(BasicMarker.java:312)

at vcf.BasicMarker.<init>(BasicMarker.java:249)

at vcf.VcfRecGTParser.<init>(VcfRecGTParser.java:70)

at vcf.BitSetGT.<init>(BitSetGT.java:74)

at vcf.VcfIt.lambda$static$7(VcfIt.java:90)

at vcf.VcfIt.lambda$new$8(VcfIt.java:192)

Do you have any suggestion for me

Many thanks

Victor

[Victor Hsu]

Hi, I dont understand why I if I use --snps-only just acgt to remove the delete SNP. My all genotype data all became to .|.

Please help me thanks

[Christopher Chang]

Can you post the full plink .log file from that run?

[Victor Hsu]

PLINK v1.90b3.46 64-bit (13 Feb 2017)

Options in effect:

  --allow-no-sex

  --bfile BoderCollieonly

  --dog

  --noweb

  --out BCB8

  --recode vcf

  --snps-only just-acgt

Hostname: login3

Working directory: /project/RDS-FSC-GPMC-RW/PLINK_file_in_house

Start time: Fri Jul  6 00:23:39 2018

Note: --noweb has no effect since no web check is implemented yet.

Random number seed: 1530800619

32094 MB RAM detected; reserving 16047 MB for main workspace.

Allocated 676 MB successfully, after larger attempt(s) failed.

2197 out of 213181 variants loaded from .bim file.

250 dogs (7 males, 0 females, 243 ambiguous) loaded from .fam.

Ambiguous sex IDs written to BCB8.nosex .

185 phenotype values loaded from .fam.

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 250 founders and 0 nonfounders present.

Calculating allele frequencies... done.

Total genotyping rate is 0.

2197 variants and 250 dogs pass filters and QC.

Among remaining phenotypes, 69 are cases and 116 are controls.  (65 phenotypes

are missing.)

--recode vcf to BCB8.vcf ... done.

[Christopher Chang]

This says "Total genotyping rate is 0", so there probably is a problem with how BoderCollieonly.bed file was created; do you have the .log for that?

[Victor Hsu]

the log file for BorderCollie bed

Options in effect:

  --allow-no-sex

  --dog

  --file BoderCollieonly

  --make-bed

  --not-chr 0 x y mt 39 40

  --noweb

  --out BoderCollieonly

Hostname: login3

Working directory: /project/RDS-FSC-GPMC-RW/PLINK_file_in_house

Start time: Fri Jul  6 00:22:34 2018

Note: --noweb has no effect since no web check is implemented yet.

Random number seed: 1530800554

32094 MB RAM detected; reserving 16047 MB for main workspace.

Allocated 676 MB successfully, after larger attempt(s) failed.

Scanning .ped file... done.

Performing single-pass .bed write (213181 variants, 250 dogs).

--file: BoderCollieonly-temporary.bed + BoderCollieonly-temporary.bim +

BoderCollieonly-temporary.fam written.

213181 variants loaded from .bim file.

250 dogs (7 males, 0 females, 243 ambiguous) loaded from .fam.

Ambiguous sex IDs written to BoderCollieonly.nosex .

185 phenotype values loaded from .fam.

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 250 founders and 0 nonfounders present.

Calculating allele frequencies... done.

Total genotyping rate is 0.875943.

213181 variants and 250 dogs pass filters and QC.

Among remaining phenotypes, 69 are cases and 116 are controls.  (65 phenotypes

are missing.)

--make-bed to BoderCollieonly.bed + BoderCollieonly.bim + BoderCollieonly.fam

... done.

Regards

Victor

[Victor Hsu]

the other log file 

Options in effect:

--dog

--noweb

--allow-no-sex

--file BigData2

--remove dog2.txt

--recode

--out Bullmastiffonly

229412 (of 229412) markers to be included from [ BigData2.map ]

Warning, found 528 individuals with ambiguous sex codes

Writing list of these individuals to [ Bullmastiffonly.nosex ]

535 individuals read from [ BigData2.ped ] 

470 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

102 cases, 368 controls and 65 missing

7 males, 0 females, and 528 of unspecified sex

Reading individuals to remove [ dog2.txt ] ... 250 read

250 individuals removed with --remove option

Before frequency and genotyping pruning, there are 229412 SNPs

285 founders and 0 non-founders found

6239 SNPs with no founder genotypes observed

Warning, MAF set to 0 for these SNPs (see --nonfounders)

Writing list of these SNPs to [ Bullmastiffonly.nof ]

Total genotyping rate in remaining individuals is nan

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 229412 SNPs

After filtering, 33 cases, 252 controls and 0 missing

After filtering, 0 males, 0 females, and 285 of unspecified sex

Writing recoded ped file to [ Bullmastiffonly.ped ] 

Writing new map file to [ Bullmastiffonly.map ] 

On Friday, 6 July 2018 06:14:00 UTC+8, Christopher Chang wrote:

[Christopher Chang]

Okay, genotyping rate is not zero there. Is it possible for you to send me the .bed+.bim+.fam fileset so I can take a closer look?

[Victor Hsu]

The files are quite big. I try to send you to your privately mail

Thanks

[Isabel Hostettler]

I would also be interested in this as I have a similar problem. After using —recode vcf bgz I get lots of „./.“

Best,

Isabel

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Christopher Chang]

Okay, the problem is that your .bim file uses 1/2/3/4 rather than A/C/G/T coding, so the only variants which pass the "--snps-only just-acgt" filter are the ones where all genotypes are missing.

--alleleACGT might solve your problem, but you should double-check that 1 really represents A, 2 really represents C, etc.

[Victor Hsu]

Thank you.

I used to use  --alleleACGT then --snps-only just-acgt once. But it did not work.

However, I will try again then let u know how is going.

[SN]

Were you able to get Beagle to work?  My input vcf files are in ACGT format and --snps-only. I am running the following command to perform imputation per chromosome:

java -Xmx50g -jar beagle.25Nov19.28d.jar gt=chr1.vcf.gz out=imputed_b37_imputed ref=chr1.1kg.phase3.v5a.b37.bref3 map=plink.chr1.GRCh37.map chrom=1 impute=true

However, I get this error after several hours of running:

ERROR: Reference and target files have no markers in common in interval: 
       1:165113264-205459274

Common markers must have identical CHROM, POS, REF, and ALT fields.
Exiting program.

 

How can I skip the intervals with no common markers and proceed with imputation without exiting the program ? Or do I have to modify my input plink files ? 

Thanks in advance for your help!