Error in step 2 of the run_dchic.sh script

[asgda]

Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) : 
  no rows to aggregate
Calls: pcselect ... aggregate -> aggregate.formula -> aggregate.data.frame
In addition: Warning message:
In cor(cbind(chrom.list[[j]], tss = pca$tss)) :
  the standard deviation is zero
Execution halted

GOT THE ABOVE ERROR WHILE RUNNING STEP2 USING THE FOLLOWING COMMAND:
Rscript dchicf.r --file input.txt --pcatype select --dirovwt T --genome hg38

I have checked that the locations are absolutely fine for each file and the genome is hg38. Also, the step 1 command gave out proper results without any errors, i.e., it created the folders with all the experiments.

Any way of resolving this error? Any help is appreciated.

[ay-lab]

For what Hi-C resolution are you running the compartment analysis?

[asgda]

The resolution is 10000 which we are using.

[ay-lab]

To ensure there is no issue with the downloaded hg38 files, can you please run the analysis at 100Kb resolution? Also, is there any non-standard chromosome in the analysis?

[asgda]

We have Y chromosome in it. Now, we will try with 100 kb resolution and see what is the output.

[Sagnik-Epigen]

I have encountered same issue.. I have tried with 100kb. Didn't work

[Sagnik-Epigen]

find a way... try to utilize eBackgroud scheme 1

[wangchen-blip]

Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) : 
  no rows to aggregate
Calls: pcselect ... aggregate -> aggregate.formula -> aggregate.data.frame
In addition: Warning message:
In cor(cbind(chrom.list[[j]], tss = pca$tss)) :
  the standard deviation is zero
Execution halted

GOT THE ABOVE ERROR WHILE RUNNING STEP2 USING THE FOLLOWING COMMAND: Rscript dchicf.r --file input.txt --pcatype select --dirovwt T --genome hg38

I have checked that the locations are absolutely fine for each file and the genome is hg38. Also, the step 1 command gave out proper results without any errors, i.e., it created the folders with all the experiments.

Any way of resolving this error? Any help is appreciated.

Calculating expected counts from chromosome wise background
Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) :
no rows to aggregate
Calls: lapply ... aggregate -> aggregate.formula -> aggregate.data.frame
停止执行