core dumped

[houruiyan]

Hi Dr chung,

I have another question.

I want to run proactiv from bam file. The bam file in the red frame was used.

This is my script

library(proActiv)
#BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")

mouse.gtf.file <- '/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/ref_annotation/Mus_musculus.GRCm38.77.gtf.gz'
mouse_annotation <- preparePromoterAnnotation(file = mouse.gtf.file, species = 'Mus_musculus')


mouse_bam_file<-'/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/bam_file/mouse/5360sTS.Mouse.Kidney.9wpb.Male.sorted.bam'

mouse_result <- proActiv(files = mouse_bam_file,
                   promoterAnnotation = mouse_annotation,genome='mm10',ncores=1)


## Removes single-exon transcripts / promoters by eliminating promoter counts that are NA 
result <- result[complete.cases(assays(result)$promoterCounts),]

## export result
result_df <- rowData(result)
result_df$txId <- vapply(result_df$txId, paste, collapse = ", ", character(1L))
write.table(result_df, "/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/proactiv_result/mouse/5360sTS.Mouse.Kidney.9wpb.Male.rowData.tsv", sep = "\t", quote = F)

result_absolutePromoterActivity_df <- assays(result)$absolutePromoterActivity
write.table(result_absolutePromoterActivity_df, "/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/proactiv_result/mouse/5360sTS.Mouse.Kidney.9wpb.Male.activ.tsv", sep = "\t", quote = F)

Then I run [ruiyanhou@CPU3:RNA_seq_organ_species]$ nohup Rscript run_proactiv.R &

But I always get this error

In addition, when I run in the Rstudio, it also aborted suddendly.

Could you help me? Thank you very much!

[houruiyan]

This solved. Thanks! When I changed to another server. this error will not appear.