Generate genotyping calls from CEL files

[dauss75]

Hello there,

Thanks for the nice tutorial!

I have calvin CEL files that were converted to text files using apt-cel-convert.
Having the text CEL files, I tried to run the command and got an error:
apt-probeset-genotype -c lib/GenomeWideSNP_6.cdf -a birdseed --read-models-birdseed lib/GenomeWideSNP_6.birdseed.models --special-snps lib/GenomeWideSNP_6.specialSNPs --out-dir apt --cel-files listfile

FATAL ERROR:TsvFile.cpp:2672: This file appears to be binary. (filename='../data/test.cel/1.CEL')

It's clear that the CEL files are not binary.
It seems the error is from birdseed, but I was wondering whether you have any thoughts on this.

Thanks,
Segun

[kaichop]

you can run Linux command "file" to check whether it is binary or text
file. Also delete this file from listfile and see whether other files have
similar issues.

On Fri, Aug 21, 2015 at 8:31 AM, Segun J [email protected] wrote:

Hello there,

Thanks for the nice tutorial!

I have calvin CEL files that were converted to text files using
apt-cel-convert.
Having the text CEL files, I tried to run the command and got an error:
apt-probeset-genotype -c lib/GenomeWideSNP_6.cdf -a birdseed
--read-models-birdseed lib/GenomeWideSNP_6.birdseed.models --special-snps
lib/GenomeWideSNP_6.specialSNPs --out-dir apt --cel-files listfile

FATAL ERROR:TsvFile.cpp:2672: This file appears to be binary.
(filename='../data/test.cel/1.CEL')

It's clear that the CEL files are not binary.

It seems the error is from birdseed, but I was wondering whether you have
any thoughts on this.

Thanks,
Segun

—
Reply to this email directly or view it on GitHub
#2.

[dauss75]

thanks for the quick reply.
I am running with only four CEL files and using the "file" command, I get:
1.CEL: data

[kaichop]

The file may be corrupt, try other CEL files to see if the same thing
occurs for other files. CEL should be a text file.

On Fri, Aug 21, 2015 at 9:04 AM, Segun J [email protected] wrote:

thanks for the quick reply.
I am running with only four CEL files and using the "file" command, I get:
1.CEL: data

—
Reply to this email directly or view it on GitHub
#2 (comment)
.

[dauss75]

I figured out the CEL files were generated based on the CytoScanHD_Array platform. Trying to convert them now.

[Vaidhy-M]

Hello there,

Thanks for the nice tutorial!

I have calvin CEL files that were converted to text files using apt-cel-convert.
Having the text CEL files, I tried to run the command and got an error:
apt-probeset-genotype -c lib/GenomeWideSNP_6.cdf -a birdseed --read-models-birdseed lib/GenomeWideSNP_6.birdseed.models --special-snps lib/GenomeWideSNP_6.specialSNPs --out-dir apt --cel-files listfile

FATAL ERROR:TsvFile.cpp:2672: This file appears to be binary. (filename='../data/test.cel/1.CEL')

It's clear that the CEL files are not binary.
It seems the error is from birdseed, but I was wondering whether you have any thoughts on this.

Thanks,
Segun

I am facing the same issue in Mapping 500K CEL files. Linux File command says the files are in Data format. Could you please explain how to fix this? Should I convert CEL files to a different format? Thanks!

[kaichop]

I cannot tell what is the problem, but perhaps you can delete this file from the listfile and try again. If there is no more error message, then perhaps this particular CEL is corrupted and treated as binary.

…

On Thu, Feb 14, 2019 at 11:47 AM Vaidhy-M ***@***.***> wrote: Hello there, Thanks for the nice tutorial! I have calvin CEL files that were converted to text files using apt-cel-convert. Having the text CEL files, I tried to run the command and got an error: apt-probeset-genotype -c lib/GenomeWideSNP_6.cdf -a birdseed --read-models-birdseed lib/GenomeWideSNP_6.birdseed.models --special-snps lib/GenomeWideSNP_6.specialSNPs --out-dir apt --cel-files listfile FATAL ERROR:TsvFile.cpp:2672: This file appears to be binary. (filename='../data/test.cel/1.CEL') It's clear that the CEL files are not binary. It seems the error is from birdseed, but I was wondering whether you have any thoughts on this. Thanks, Segun I am facing the same issue in Mapping 500K CEL files. Linux File command says the files are in Data format. Could you please explain how to fix this? Should I convert CEL files to a different format? Thanks! — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuORyBkzNr0vaT_3ZgxUll-BoncZlks5vNZMtgaJpZM4Fv9rz> .