I have an issue and I would like your advice on it.
My dataset is composed of 3437 individuals placed in 376 families. I do not have genomic data from the Grandparents.
The SNP set is composed of 51100 SNPs
None of those SNPs are considered to be informative by ParentCall2.
Plus many individuals are set to "all missing" despite being in the vcf file.
Do you think that the issue could come from :
1)All the SNP are non-informative because the family size is too low ?
2)There is an issue with the VCF files (that I generated with Plink) ?
I added the Pedigree and the first lines of the .vcf files.
Thank you for your question, you are not annoying at all!
It seems the individual names in the vcf and pedigree do not match. All the names in the vcf have underscore _ like 40821467912064082140401641_4112182101227 but the names in pedigree don't have it.
As such, no data from the vcf file is obtained. To fix this problem, you have to figure the correct individual names.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-02-06
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello Pasi,
Small question : does Filtering2 as a limitation on the size of the ID of the individual ?
The PartentCall2 works perfectly but when I ran the Filtering2 module, I have the following Java Error :
Number of individuals = 3437
Number of families = 376
java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 60
at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:55)
at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:52)
at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:213)
at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:210)
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:98)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Preconditions.java:112)
at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Preconditions.java:349)
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4602)
at java.base/java.lang.String.substring(String.java:2715)
at DataParser.getNextLine(DataParser.java:711)
at DataParser.getNextLine(DataParser.java:650)
at Filtering2.filter(Filtering2.java:160)
at Filtering2.main(Filtering2.java:621)
Error 504
Error: Unable to load input file or errors in the file
As the file used is created by ParentlCall2, I am trying to understand, if they are issue in the format of the data itself that would create such bug.
Many thanks for your help,
Julien.
Last edit: Recoquillay Julien 2024-02-14
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The Parenttest.txt might be a wrong file for this purpose. How did you produced it? Based on the name, I would think it is not the ouput from ParentCall2?
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Pasi,
The Parenttest.txt comes from ParentCall2.
I tried to rename it p.call as in your example in the wiki but it had not effect.
Do you think that re-runing the ParentCall2 but with p.call as the output file will be better ?
Thanks,
Julien.
EDIT : I re-launched the ParentCall2 analysis with this command :
nohup java -cp /home/julien/lep-map3/bin ParentCall2 data=PedFormatLep3p.txt vcfFile=mapf2.vcf > p.call
EDIT2 :
Command after run of command in EDIT :
java -cp /home/julien/lep-map3/bin Filtering2 data=p.call dataTolerance=0.001
Give the same error than shown in previous messages.
Last edit: Recoquillay Julien 2024-02-20
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The file is corrupted (due to nohup?). The ParentCall2 output from out and error streams are mixed. Run ParentCall2 without nohup (or add extra parenthesis so that this does not occur).
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Greetings Pasi,
Sorry to annoy you again.
I have an issue and I would like your advice on it.
My dataset is composed of 3437 individuals placed in 376 families. I do not have genomic data from the Grandparents.
The SNP set is composed of 51100 SNPs
None of those SNPs are considered to be informative by ParentCall2.
Plus many individuals are set to "all missing" despite being in the vcf file.
Do you think that the issue could come from :
1)All the SNP are non-informative because the family size is too low ?
2)There is an issue with the VCF files (that I generated with Plink) ?
I added the Pedigree and the first lines of the .vcf files.
Many thanks,
Julien.
Last edit: Recoquillay Julien 2024-02-05
Dear Julien,
Thank you for your question, you are not annoying at all!
It seems the individual names in the vcf and pedigree do not match. All the names in the vcf have underscore
_like 40821467912064082140401641_4112182101227 but the names in pedigree don't have it.As such, no data from the vcf file is obtained. To fix this problem, you have to figure the correct individual names.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-02-06
I feel dumb...As I never used vcf, I though it was a normal that the ID became "Family-ID_Individual-ID" after the conversion.
Thanks again for answering such trivial things...
I am happy to help,
Cheers,
Pasi
Hello Pasi,
Small question : does Filtering2 as a limitation on the size of the ID of the individual ?
The PartentCall2 works perfectly but when I ran the Filtering2 module, I have the following Java Error :
Number of individuals = 3437
Number of families = 376
java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 60
at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:55)
at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:52)
at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:213)
at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:210)
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:98)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Preconditions.java:112)
at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Preconditions.java:349)
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4602)
at java.base/java.lang.String.substring(String.java:2715)
at DataParser.getNextLine(DataParser.java:711)
at DataParser.getNextLine(DataParser.java:650)
at Filtering2.filter(Filtering2.java:160)
at Filtering2.main(Filtering2.java:621)
Error 504
Error: Unable to load input file or errors in the file
As the file used is created by ParentlCall2, I am trying to understand, if they are issue in the format of the data itself that would create such bug.
Many thanks for your help,
Julien.
Last edit: Recoquillay Julien 2024-02-14
Dear Julien,
Could you send me the Filtering2 command line you have run?
Cheers,
Pasi
Of course I used the following command :
java -cp /home/julien/lep-map3/bin Filtering2 data=/ark/users/julien/projects/LinkageMap/Parenttest.txt dataTolerance=0.001 > Filtering.txt
Last edit: Recoquillay Julien 2024-02-19
Dear Julien,
The Parenttest.txt might be a wrong file for this purpose. How did you produced it? Based on the name, I would think it is not the ouput from ParentCall2?
Cheers,
Pasi
Hi Pasi,
The Parenttest.txt comes from ParentCall2.
I tried to rename it p.call as in your example in the wiki but it had not effect.
Do you think that re-runing the ParentCall2 but with p.call as the output file will be better ?
Thanks,
Julien.
EDIT : I re-launched the ParentCall2 analysis with this command :
nohup java -cp /home/julien/lep-map3/bin ParentCall2 data=PedFormatLep3p.txt vcfFile=mapf2.vcf > p.call
EDIT2 :
Command after run of command in EDIT :
java -cp /home/julien/lep-map3/bin Filtering2 data=p.call dataTolerance=0.001
Give the same error than shown in previous messages.
Last edit: Recoquillay Julien 2024-02-20
Hi Julien,
Can you share a few lines of your parentTest.txt ? Like 10-20 first lines?
Cheers,
Pasi
Last edit: Pasi Rastas 2024-02-20
Of course,
Here are attached the first 50 lines.
The file is corrupted (due to nohup?). The ParentCall2 output from out and error streams are mixed. Run ParentCall2 without nohup (or add extra parenthesis so that this does not occur).
Cheers,
Pasi
Thanks Pasi.
Trying it right now.
EDIT : Situation solved. Thanks Pasi. Until the next :D
Last edit: Recoquillay Julien 2024-02-22