carmenmacr11
commented
1 year ago as it says from the mash repository, i can't run the mash model neither with my data nor with the data from data/fasqtl/ Tissue_1.fastqtl.gz Tissue_2.fastqtl.gz When I use the example, the folder /fastqtl_to_mash_output is generated which contains these files: FastQTLSumStats.h5 FastQTLSumStats.mash.rds FastQTLSumStats.portable.log FastQTLSumStats.log FastQTLSumStats.portable.h5 Tissue_1.fastqtl.h5 Tissue_2.fastqtl.h5 I use the FastQTLSumStats.mash.rds file to perform the mash model (this is what's inside): Length Class Mode random.z 36 -none- numeric random.test.z 36 -none- numeric strong.z 8 -none- numeric random.b 36 -none- numeric random.test.b 36 -none- numeric strong.b 8 -none- numeric random.s 36 -none- numeric random.test.s 36 -none- numeric strong.s 8 -none- numeric
then I switch to docker to do the mash analysis and run it, and I run this command: fastqtl2mash-singularity sos run mashr_flashr_workflow.ipynb mash --data ../fastqtl_to_mash_output/FastQTLSumStats.mash.rds and I get the error: ERROR: flash_nonneg (id=831e2a240d34d36d) returns an error. ERROR: pca (id=cd2135596b55fb49) returns an error. ERROR: vhat_simple (id=a6a6ac2bd80c0140) returns an error. ERROR: flash (id=16103308e4081ad1) returns an error. when I use my own data, this is the summary
summary(data) Length Class Mode random.z 4 -none- numeric random.test.z 5 -none- numeric strong.z 1 -none- numeric random.b 4 -none- numeric random.test.b 5 -none- numeric strong.b 1 -none- numeric random.s 4 -none- numeric random.test.s 5 -none- numeric strong.s 1 -none- numeric
it gives me the same error
Hello, I am attempting to replicate your workflow, but I was wondering if you perform any preliminary steps with the MatrixEQTLSumStats.Portable.Z.rds file. When I use the example data/fasqtl and process it through mash using your scripts, it produces a different rds file that doesn't work when used to execute mash. Similarly, with my own example, it doesn't work even though I follow all the steps as instructed. I pass the data from tensorQTL to mash, but it gives me the following error when I run mashr_flashr_workflow.ipynb:
fastqtl2mash-singularity sos run mashr_flashr_workflow.ipynb mash --data ../data/FastQTLSumStats.mash.rds and it gives me the following error: INFO: Running vhat_mle: V estimate: "mle" method INFO: Running pca: INFO: Running flash_nonneg: Perform FLASH analysis with non-negative factor constraint (time estimate: 20min) INFO: Running vhat_simple: V estimate: "simple" method (using null z-scores) INFO: Running flash: Perform FLASH analysis with non-negative factor constraint (time estimate: 20min) ERROR: flash_nonneg (id=831e2a240d34d36d) returns an error. ERROR: pca (id=cd2135596b55fb49) returns an error. ERROR: vhat_simple (id=a6a6ac2bd80c0140) returns an error. ERROR: flash (id=16103308e4081ad1) returns an error.