StatFunGen
Bug in running univariate fine mapping
There is a bug when I am trying to run mnm_regression.ipynb, which works well at the end of July. I did not see obvious update in recent modification in that pipeline, could be some updates in pecotmr?
Dimension of input genotype data is 806 rows and 19076 columns for genomic region of chr17:42560179-46679816 Follow-up on region because signals above PIP threshold 0.025 were detected in initial model screening. Total time elapsed for susie_wrapper: 4.362 Number of variants dropped: 8653 out of 19076 total variants. Total time elapsed for susie_wrapper: 0.410000000000004 Type of analysis performed: st-blr-individual-level-dense-ld Type of analysis performed: st-blr-individual-level-dense-ld Randomly selecting 5000 out of 5000 input variants for cross validation purpose. Error in (function (.x, .f, ..., .progress = FALSE) : ℹ In index: 1. Caused by error in
`*tmp*`[, i]: ! subscript out of bounds Calls: lapply ... resolve.list -> signalConditionsASAP -> signalConditions Execution halted
oh boy, this is the cross validation for TWAS which underwent some changes as @Chunmingl works on the multivariate version.
I think we need a MWE for this -- could you save the data in question using --save-data option and also extract the code from the log file that reproduce the issue, then we communicate it on slack with Chunming?
