run code error

[ZgtL15]

Hi! Thank you the excellent pipline, it's really useful, but when i try to use it on a big cohort (>1000 samples), it meets an error.

Creating merged peak sets in output directory /path/xxxx/xxxx
ATAC_cohort
Error in convergeClusterGRanges(., by = "score", decreasing = T) :
object 'gr_all' not found
Calls: extendedPeakSet ... lapply -> lapply -> FUN -> %>% -> convergeClusterGRanges
Execution halted

this is my code,
Rscript createIterativeOverlapPeakSet.R --metadata /path/file.txt --macs2dir /path/QC_pass_sample_summit_macs2/ --outdir /path/consensus_peak/ --suffix _summits.bed --blacklist /path/hg19-blacklist.v2.bed --genome hg19 --spm 5 --rule "2" --extend 250

do you have any idea about it?

[eafyounian]

@ZgtL15 Hi! Were you able to solve the issue? If yes, can you please share? :)

I get the same error using only 40 samples. However, when I ran it over 6 samples (3 samples per group), it worked just fine...