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sQTL association analysis in job `8eaa4402df95e92a` on opcenter 23.22.157.8 showing > ERROR: cis_1 (id=8eaa4402df95e92a) returns an error. > ERROR: [cis_1]: [0]: > Failed to execute python /home/bst2126/output/cis_1_0_258db4a1.py > exitcode=139, workdir=/home/bst2126/data,...

* in snp is not allowed in MASH pipeline `rds_to_vcf`

6

There are some "*" (which means a deletion) in snp file will cause the error `Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 42 (char '*') not in lookup table` That...

Different result from available results

2

I am reproducing the MASH pipeline, and I found the result of `mashr` is different from the available results (produced by Hao), the code in this step is > library(mashr)...

How to deal with NA column in MASH analysis

1

When I was trying to Compute MASH posteriors in MASH analysis, there is a NA column in bhat and sbhat matrix in file `/mnt/vast/hpc/csg/rf2872/Work/MASH_csg.q/output/RDS/ALL_Ast_End_Exc_Inh_Mic_OPC_Oli.log2cpm.bed.processed_phenotype.per_chrom_ALL_Ast_End_Exc_Inh_Mic_OPC_Oli.log2cpm.ALL_Ast_End_Exc_Inh_Mic_OPC_Oli.covariate.pca.resid.PEER.cov.chr9.norminal.cis_long_table.RMI1.rds`, which is a split rds file...

Bug in running univariate fine mapping

1

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...

We put the rare events detection in phenotype imputation pipeline for now, as we need to do imputation first and then normalization.In principle this should be put into normalization part,...

There is a bug showing customer windows are not uniquely mapped to phenotype data, which should be fixed as it should not be an error to stop the work, we...