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SHZ66 / zinba

Automatically exported from code.google.com/p/zinba
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*** caught segfault *** address 0x3604eb2, cause 'memory not mapped' #65

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
ubuntu 12.04

2) What error message was displayed?
 *** caught segfault ***
address 0x3604eb2, cause 'memory not mapped'

3) What was the exact command you used that resulted in the error?
library(zinba) 
generateAlignability(
  mapdir='map50_files/',
  outdir='ATAC_zinba/',
  athresh=1,
  extension=200,
  twoBitFile='mm10.2bit'
)

4) Please copy and paste any additional screen output that resulted from
running the command
Processing Mus_musculus.GRCm38.69.dna.chromosome.10b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.10 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.11b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.11 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.12b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.12 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.13b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.13 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.14b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.14 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.15b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.15 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.16b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.16 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.17b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.17 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.18b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.18 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.19b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.19 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.1b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.1 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.2b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.2 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.3b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.3 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.4b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.4 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.5b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.5 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.6b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.6 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.7b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.7 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.8b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.8 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.9b.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.9 .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.MTb.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.MT .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.Xb.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.X .......

Processing Mus_musculus.GRCm38.69.dna.chromosome.Yb.out .......
    Mus_musculus.GRCm38.69.dna.chromosome.Y .......

Processing Mus_musculus.GRCm38.69.dna.nonchromosomalb.out .......
    Mus_musculus.GRCm38.69.dna.nonchromosomal .......

Processing Mus_musculus.GRCm38.69.dna.nonchromosomalb.out .......
    Mus_musculus.GRCm38.69.dna.nonchromosomal .......
Loading align count data from 
/home/ashwini.jeggari/ATAC_ZINBA/map50_files/temp.wig
    Processing Mus_musculus.GRCm38.69.dna.chromosome.10

 *** caught segfault ***
address 0x3604eb2, cause 'memory not mapped'

Traceback:
 1: .C("alignAdjust", as.character(inputfile), as.character(outDir),     as.character(twoBitFile), as.integer(athresh), as.integer(adjustsize),     PACKAGE = "zinba")
 2: alignAdjust(inputfile = paste(mapdir, "temp.wig", sep = ""),     outDir = outdir, twoBitFile = twoBitFile, athresh = athresh,     adjustsize = round(extension/2))
 3: generateAlignability(mapdir = "/home/ashwini.jeggari/ATAC_ZINBA/map50_files/",     outdir = "/home/ashwini.jeggari/ATAC_ZINBA/align_athresh1_extension200",     athresh = 1, extension = 200, twoBitFile = "/home/ashwini.jeggari/ATAC_ZINBA/mm10.2bit")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Original issue reported on code.google.com by ashwini....@gmail.com on 14 Jul 2014 at 10:28

GoogleCodeExporter commented 8 years ago 
I saw the similar kind of posts regarding this issue. But none have mentioned 
about the cause and how to solve it. Would be great if someone help me in 
solving this error. 
Thanks!

Original comment by ashwini....@gmail.com on 14 Jul 2014 at 10:30

GoogleCodeExporter commented 8 years ago 
I had this problem too. It was solved after I installed the mulicore package 
manually.

Original comment by slykua...@gmail.com on 14 Jan 2015 at 4:04