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gusevlab / fusion_twas

methods for functional summary-based imputation
http://gusevlab.org/projects/fusion/
GNU General Public License v3.0
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Trying to create own weights : error with TMP #60

Open ChristianDina opened 1 year ago

ChristianDina commented 1 year ago

Hi,

I am trying to build my own weights with a bed/bim/fam file and receive the error below. I am not sure by the wya what the $TMP is supposed to be. - didn't find the definition, sorry if I missed it. If I create one the error is "cannot remove" and if I do not, the error is "does not exist".

And by the way, I understood that the expression data has to be in the fam file ... is that correct ?

Thanks a lot for your help

Christian

############## ERROR ########################

TMP does not exist, likely GCTA could not converge, skipping gene Warning message: In system(arg, ignore.stdout = SYS_PRINT, ignore.stderr = SYS_PRINT) : error in running command (

ChristianDina commented 1 year ago

I have solved this but still finds it very tedious to go through the sh codes to understand how to to. For instance, has anybody created .pos file ? I see how to create it but wa wondering whether there was something ready.

liuzh233 commented 8 months ago

I also encountered this problem when calculating the weight of my data. I would like to ask you how to solve it. Can you teach me? Thank you so much.

NancyLSH commented 6 months ago

I also have the same problem when calculating my weight, do you solve the problem?

Ruwanmali commented 3 months ago

Hi,

I also have the same error. I would like to know if anyone has a solution for this issue. I appreciate your help.

lashoushou commented 3 months ago

Hello, I'd like to ask you how you solved this problem.

lashoushou commented 3 months ago

I'm bored to death with this question /(ㄒoㄒ)/~~

lashoushou commented 3 months ago

I found something useful at https://github.com/opain/Calculating-FUSION-TWAS-weights-pipeline/blob/master/README.md

alyssacl commented 2 months ago

I have solved this but still finds it very tedious to go through the sh codes to understand how to to. For instance, has anybody created .pos file ? I see how to create it but wa wondering whether there was something ready.

Hello, did you have to create this yourself, or was it generated somehow? I have all my weights now, but no .pos file. Thank you, Alyssa

Miles823 commented 1 month ago

I have solved this but still finds it very tedious to go through the sh codes to understand how to to. For instance, has anybody created .pos file ? I see how to create it but wa wondering whether there was something ready.

For the .pos file, You can see the example output in the "wget https://data.broadinstitute.org/alkesgroup/FUSION/WGT/GTEx.Whole_Blood.tar.bz2", just build your file as the example file. Moreover, Can you please talk about how you solve the problem in the TCGA could not converge.

sitahoo commented 1 month ago

I have solved this but still finds it very tedious to go through the sh codes to understand how to to. For instance, has anybody created .pos file ? I see how to create it but wa wondering whether there was something ready.

For the .pos file, You can see the example output in the "wget https://data.broadinstitute.org/alkesgroup/FUSION/WGT/GTEx.Whole_Blood.tar.bz2", just build your file as the example file. Moreover, Can you please talk about how you solve the problem in the TCGA could not converge.

Hi,i read the script，and after that i set the parameter --hsq_set and it seems go on，but then i had another problem. So i guess i should figure out how actually the pipline work.

Miles823 commented 1 month ago

I have solved this but still finds it very tedious to go through the sh codes to understand how to to. For instance, has anybody created .pos file ? I see how to create it but wa wondering whether there was something ready.

For the .pos file, You can see the example output in the "wget https://data.broadinstitute.org/alkesgroup/FUSION/WGT/GTEx.Whole_Blood.tar.bz2", just build your file as the example file. Moreover, Can you please talk about how you solve the problem in the TCGA could not converge.

Hi,i read the script，and after that i set the parameter --hsq_set and it seems go on，but then i had another problem. So i guess i should figure out how actually the pipline work.

Hi, Yeas, we can set the --hsp_set, it means we set the heritability for this genes without calculating. Maybe I also should try this way. or make the groups size bigger.