search

tgac-vumc / ACE

Absolute Copy Number Estimation using low-coverage whole genome sequencing data
14 stars 6 forks source link

'Realloc' could not re-allocate memory (18446744065128005632 bytes) #4

Closed shashwatsahay closed 1 week ago

shashwatsahay commented 3 years ago

Hi

I keep getting this error everytime I try to run ACE

I am using R 4.1.0 inside a conda environment

All other dependent packages were directly downloaded using biocManger

Loaded bin annotations for genome ‘hg19’, bin size 100 kbp, and experiment type ‘SR50’ from annotation package QDNAseq.hg19 v0.99.2
    tumor-bone-marrow-0X_XXX_merged.mdup (1 of 1): extracting reads ...Error in value[[3L]](cond) :
  'Realloc' could not re-allocate memory (18446744065128005632 bytes)
  file: /pathtobam/tumor-bone-marrow-0X_XXX_merged.mdup.bam
  index: NA
Calls: runACE ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
jpoell commented 1 year ago

Sorry I was not notified and have only responded to direct e-mails! This seems to be a QDNAseq problem, and it seems to have to do with the extreme memory allocation. It must be something about the bam file, but I can't imagine the size of it is several thousand petabytes. Unfortunately it is quite complicated (for me) to figure out how QDNAseq processes the bam-files, so I would suggest contacting them. I would suggest to provide some info on the bam-file (size, reads, perhaps even the header)

shashwatsahay commented 1 week ago

Hi

I just had a look at QDNAseq apparently we need to pass chumksize to bin count will have a look

https://github.com/ccagc/QDNAseq/issues/100