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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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error in CallCNVs function #43

Open lmanchon opened 3 years ago

lmanchon commented 3 years ago

Error in CallCNVs(x = all.exons, transition.probability = trans_prob, : Chromosome, start and end vector must have the same lengths.

my bed file seems to be well tabulated as:

chr1 69090 70008 OR4F5 chr1 450739 451678 OR4F16 chr1 450739 451678 OR4F29 chr1 450739 451678 OR4F3 chr1 685715 686654 OR4F16 chr1 685715 686654 OR4F29 chr1 685715 686654 OR4F3 chr1 925941 926013 SAMD11 chr1 930154 930336 SAMD11 chr1 931038 931089 SAMD11

what's wrong ?

DrChN commented 2 years ago

I amstuck up with the same error Error in CallCNVs(x = all.exons, transition.probability = 10^-4, chromosome = ExomeCount.dafr$chromosome, : Chromosome, start and end vector must have the same lengths.

where exactly i have to checkto rectify it!

Maroua2906 commented 2 years ago

Hi , I would like please to know if you have resolved this issue. I'm getting the same error message. Thank you for your help

DrChN commented 2 years ago

Yes, it is resolved... I think it is with the file format.. I will let you now tomorrow

On Sun, 4 Sep 2022, 1:23 am Maroua2906, @.***> wrote:

Hi , I would like please to know if you have resolved this issue. I'm getting the same error message. Thank you for your help

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Gedofs commented 1 year ago

HELLO GUYS! I'm wondering if you could fix the error. I'M CURRENTLY IN THE SAME SITUATION

Screenshot 2023-01-11 at 13 06 38
DrChN commented 1 year ago

Hi... check if you have same number of entries in the Chrome start and end positions...

On Thu, 12 Jan 2023, 12:37 am Gerardo Fabián, @.***> wrote:

HELLO GUYS! I'm wondering if you could fix the error. I'M CURRENTLY IN THE SAME SITUATION [image: Screenshot 2023-01-11 at 13 06 38] https://user-images.githubusercontent.com/94254364/211895752-60a8bb4f-b647-4e51-bf84-8c5af001f50a.png

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Gedofs commented 1 year ago

Thanks, that was a helpful comment. Indeed all columns have the same entry, however i could spot the error. My problem was with one of my objects and I could fix it.

El mié, 11 ene 2023 a la(s) 18:55, DrChN @.***) escribió:

Hi... check if you have same number of entries in the Chrome start and end positions...

On Thu, 12 Jan 2023, 12:37 am Gerardo Fabián, @.***> wrote:

HELLO GUYS! I'm wondering if you could fix the error. I'M CURRENTLY IN THE SAME SITUATION [image: Screenshot 2023-01-11 at 13 06 38] < https://user-images.githubusercontent.com/94254364/211895752-60a8bb4f-b647-4e51-bf84-8c5af001f50a.png

— Reply to this email directly, view it on GitHub < https://github.com/vplagnol/ExomeDepth/issues/43#issuecomment-1379356221>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AWVFMFKAADKSECWVYNPLLILWR4AG7ANCNFSM463JZ5FQ

. You are receiving this because you commented.Message ID: @.***>

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mnb29 commented 1 year ago

Hi Gedofs,

Would it be possible for you to elaborate on the object that was causing the error and how you fixed it? I am having the same issue and my bed file entries are all the same length.

DrChN commented 1 year ago

Hai... check if the bam file file and my.bed variable are run with the same bed file

On Sat, 8 Jul 2023, 12:26 am mnb29, @.***> wrote:

Hi Gedofs,

Would it be possible for you to elaborate on the object that was causing the error and how you fixed it? I am having the same issue and my bed file entries are all the same length.

— Reply to this email directly, view it on GitHub https://github.com/vplagnol/ExomeDepth/issues/43#issuecomment-1625896401, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWVFMFNHQW6TMP5STEU73C3XPBLUDANCNFSM463JZ5FQ . You are receiving this because you commented.Message ID: @.***>