hh550.hg18.pfb is missing

[wenjia2018]

Hi there,

I just tried to run the example, but i got an error message

ERROR: cannot read from pfb file ../lib/hh550.hg18.pfb: No such file or directory

Then i checked the ../lib folder, there are only two files: hh550.hmm and hhall.hmm but no .pfb files.

Could you please help me to figure out how to solve this problem?

Thanks!

[kaichop]

Unless you are using HH550 array, you should not use this PFB file. Just create one yourself using your array type and the compile_pfb.pl program.

On Thu, Feb 20, 2020 at 7:47 AM wenjia2018 notifications@github.com wrote:

Hi there,

I just tried to run the example, but i got an error message

ERROR: cannot read from pfb file ../lib/hh550.hg18.pfb: No such file or directory

Then i checked the ../lib folder, there are only two files: hh550.hmm and hhall.hmm but no .pfb files.

Could you please help me to figure out how to solve this problem?

Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/52?email_source=notifications&email_token=ABNG3OGQPXHFW6DF63HRHELRDZ3URA5CNFSM4KYOC7D2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IO7GOIA, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCFMOKC4SN33BRI2B3RDZ3URANCNFSM4KYOC7DQ .

[wenjia2018]

Dear Dr.Wang,

Thanks for your quick response.

Actually I am not sure which .pfb file I should use. I got some human genotyping data from Illumina omni1 and omni2.5 chips, which is in Plink format and there is no LRR and BAF.

1. i have to calculate LRR and BAF which are the input for PennCNV (still trying to figure out how to do this, not possible to ask the data provider to provide.)
2. then after I got LRR and BAF i could use PennCNV, but I am not sure which pfb file i coule use. I will check this function compile_pfb.pl to see if I could http://compile_pfb.pl

Thanks a lot!

Kai Wang notifications@github.com 于2020年2月20日周四 下午4:02写道：

Unless you are using HH550 array, you should not use this PFB file. Just create one yourself using your array type and the compile_pfb.pl program.

On Thu, Feb 20, 2020 at 7:47 AM wenjia2018 notifications@github.com wrote:

Hi there,

I just tried to run the example, but i got an error message

ERROR: cannot read from pfb file ../lib/hh550.hg18.pfb: No such file or directory

Then i checked the ../lib folder, there are only two files: hh550.hmm and hhall.hmm but no .pfb files.

Could you please help me to figure out how to solve this problem?

Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/WGLab/PennCNV/issues/52?email_source=notifications&email_token=ABNG3OGQPXHFW6DF63HRHELRDZ3URA5CNFSM4KYOC7D2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IO7GOIA , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNG3OCFMOKC4SN33BRI2B3RDZ3URANCNFSM4KYOC7DQ

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/52?email_source=notifications&email_token=AK7KKCEM2FRUPZSM25JISELRD2LQBA5CNFSM4KYOC7D2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMON52Q#issuecomment-589094634, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK7KKCGMLWILE3XXMB25RB3RD2LQBANCNFSM4KYOC7DQ .

-- Best Regards,

Wenjia

[kaichop]

Just create one yourself using your array type and the compile_pfb.pl program

On Thu, Feb 20, 2020 at 10:26 AM wenjia2018 notifications@github.com wrote:

Dear Dr.Wang,

Thanks for your quick response.

Actually I am not sure which .pfb file I should use. I got some human genotyping data from Illumina omni1 and omni2.5 chips, which is in Plink format and there is no LRR and BAF.

1. i have to calculate LRR and BAF which are the input for PennCNV (still trying to figure out how to do this, not possible to ask the data provider to provide.)
2. then after I got LRR and BAF i could use PennCNV, but I am not sure which pfb file i coule use. I will check this function compile_pfb.pl to see if I could http://compile_pfb.pl

Thanks a lot!

Kai Wang notifications@github.com 于2020年2月20日周四 下午4:02写道：

Unless you are using HH550 array, you should not use this PFB file. Just create one yourself using your array type and the compile_pfb.pl program.

On Thu, Feb 20, 2020 at 7:47 AM wenjia2018 notifications@github.com wrote:

Hi there,

I just tried to run the example, but i got an error message

ERROR: cannot read from pfb file ../lib/hh550.hg18.pfb: No such file or directory

Then i checked the ../lib folder, there are only two files: hh550.hmm and hhall.hmm but no .pfb files.

Could you please help me to figure out how to solve this problem?

Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <

https://github.com/WGLab/PennCNV/issues/52?email_source=notifications&email_token=ABNG3OGQPXHFW6DF63HRHELRDZ3URA5CNFSM4KYOC7D2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IO7GOIA

, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABNG3OCFMOKC4SN33BRI2B3RDZ3URANCNFSM4KYOC7DQ

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-- Best Regards,

Wenjia

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