Error in Gene_Centric_Coding analysis

[pelinunal]

Dear Xihao,

While I performed _Gene_CentricCoding analysis, the error below showed up and there were no outputs for some arrayid.

Error in seqGetData(genofile, paste0(Annotation_dir, Annotation_name_catalog$dir[which(Annotation_name_catalog$name ==  : 
  The GDS node "annotation/info/FunctionalAnnotation/genecode_comprehensive_exonic_category" does not exist.

There was no output from every arrayid but I thought it might run the code with the existing output files. I performed the STAARpipelineSummary Gene Centric Coding analysis and got this error:

Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: Gene_Centric_Coding_Results_Summary -> get -> load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '..../Gene_Centric_Coding_1.Rdata', probable reason 'No such file or direc$
Execution halted

I have the same problem with _Gene_CentricNoncoding, Sliding Window, and Dynamic Window analysis. However, there was no problem with the individual analysis.

I hope you can help me :)

Thank you! Pelin

[xihaoli]

Hi Pelin,

Thank you for your questions. For _Gene_CentricCoding analysis, have you prepared your genotype and annotation data into a single AGDS file one per chromosome, following the FAVORannotator steps?

Best, Xihao

[pelinunal]

Hi Xihao, Thank you for your quick response!

I have prepared the single aGDS file per chr by following your tutorial steps. I downloaded annotation data from FAVORannotator's database (containing 20 essential annotation scores) in CSV format​. However, it seems the problem is with some chunk chr files which are empty. Thank you made me notice! I will download again the FAVOR files and perform the analysis from the beginning.

Have a good day! Bests, Pelin

[xihaoli]

Hi Pelin,

You're very welcome. Before re-downloading the FAVOR files, could you please do a quick check for one of your aGDS file that caused the issue of

The GDS node "annotation/info/FunctionalAnnotation/genecode_comprehensive_exonic_category" does not exist

You may check this by pasting the output here using

library(SeqArray)
genofile <- seqOpen("/path_to_the_file/chr1.gds") # suppose chromosome 1 aGDS file has the issue above
genofile

Best, Xihao

[pelinunal]

Dear Xihao,

I have checked each chromosome aGDS file as you suggested and there is no error, all of them are readable as formal class SeqVarGDSClass.

Bests, Pelin

[xihaoli]

Hi Pelin,

Thanks for checking. In this case, could you please paste (1) the output of running the above 3 lines of scripts and (2) a screenshot of your Annotation_name_catalog file? This would help me better understand why genecode_comprehensive_exonic_category does not exist in your aGDS file.

Alternatively, you may send this information via email. Hope this helps.

Best, Xihao