Step 2 failed with missing input file

[Joey-Xue]

Thanks for producing this tool and the detailed documentation, which is really beginner-friendly! I got error when trying to execute the get_RVBurdenMatrix_gnomAD_rvexcaliber.clean.sh in step 2, specifically, here's the error I got:

Input variables successfully entered. Proceeding...


Error: the gnomAD rare variant burden matrix that will be generated must correspond to an internal study dataset


Please ensure that:


1) the specified naming criteria (i.e. 'internal_dataset') and all filtering criteria (i.e. 'gnomAD_MAF_theshold', 'MCAP_threshold', 'eth', and 'coverage') are consistent with what was used in the 'get_RVBurdenMatrix_internal_rvexcaliber.clean.sh' script
and
2) the specified output directory (i.e. 'outdir') contains the rare variant burden matrix for the internal study dataset that was generated in the 'get_RVBurdenMatrix_internal_rvexcaliber.clean.sh' script

Through checking the script, I found this error was due to the missing of '${internal_dataset}RVBurdenMatrix${MAF_MCAP}${eth}${coverage}.txt.gz' file, which I don't have in my out_dir. However, the output from running 1A script looked fine:

Input variables successfully entered. Proceeding...


Cross-referencing variants with gnomAD PASS sites
Warning: At least 2556 duplicate IDs in --extract file.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.


No coverage intersection selected. Will not intersect test39 with gnomAD high coverage coding regions


Initiating refGene, gnomAD_211, and dbNSFP M-CAP annotations for test39

And here's all the files from my 1A run:

ls RV_EXout/
test39.annovarInput    test39_preprocessed.bed  test39_preprocessed.fam  test39_preprocessed.nosex
test39.annovar.output  test39_preprocessed.bim  test39_preprocessed.log

Do you know why my 1A run didn't generate the expected BurdenMatrix file? It seems that the run stopped right after the annotation step
Thanks in advance for any help!