I am trying to run the Bioconductor QUASR package on multiple nodes. However, when I exceed 3 nodes in the command "cl<-makeCluster(4)", I get the following error:
Error in checkForRemoteErrors(val) : one node produced an error: Error on ip-172-31-10-100 processing sample /home/ubuntu/RtmpFNTEl1/M1_L001_R1_001.fastq.gz6bcc701726.fastq : failed to open SAM/BAM file.
After running the following commands:
library(QuasR) library(snow) library(parallel) cl<-makeCluster(4) sampleFile2<-("sample_file.txt") genomeFile<-("reference_genome.fa") proj2 <- qAlign(sampleFile2, genomeFile, paired="no", cacheDir="/home/ubuntu",clObj=cl)
Reading threads from similar errors from this list, the explanation that makes the most sense to me is that QUASR is losing it's connection to the child R process or that multiple nodes are trying to access/write sam files to the same folder.