search

LuyiTian / scPipe

a pipeline for single cell RNA-seq data analysis
69 stars 24 forks source link

segfault: Memory not mapped #60

Open MingBit opened 6 years ago

MingBit commented 6 years ago

Hey, I got this issue when I was testing it. Anything I could try to fix it? Thanks a lot.

caught segfault address 0x30, cause 'memory not mapped'

Traceback: 1: .Call("_scPipe_rcpp_sc_exon_mapping", PACKAGE = "scPipe", inbam, outbam, annofn, am, ge, bc, mb, bc_len, UMI_len, stnd, fix_chr) 2: rcpp_sc_exon_mapping(inbam, outbam, annofn, bam_tags$am, bam_tags$ge, bam_tags$bc, bam_tags$mb, bc_len, UMI_len, stnd, fix_chr) 3: sc_exon_mapping(file.path(data_dir, "out.aln.bam"), file.path(data_dir, "out.map.bam"), ERCCanno_fn) An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped)

Shians commented 6 years ago

This is currently an issue with non-ENSEMBL annotations, are you using a non-ENSEMBL annotation?

MingBit commented 6 years ago

Thanks for response. I was using this one: Mus_musculus.GRCm38.dna.primary_assembly.fasta Download from ftp://ftp.ensembl.org/pub/release-91/fasta/mus_musculus/dna/

Shians commented 6 years ago

Did you put that into the annofn argument? For the annotation you should be using a GFF3 file from ENSEMBL, so in your case you can download ftp://ftp.ensembl.org/pub/release-91/gff3/mus_musculus/Mus_musculus.GRCm38.91.gff3.gz and unzip it.