Thread: Erange
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Old 04-24-2009, 09:24 AM   #10
griffon42
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Location: New York

Join Date: Jan 2009
Posts: 23
Default ERANGE error message

Hi all-

I've used successfully used ERANGE3.0.1 in the past for some RNA-seq analysis. I'm now running into some problems getting through the RunStandardAnalysis script.

My reads are Bowtie-aligned (single-end) and built into an appropriate RDS file. I'm working with the mouse genome.

When running RunStandardAnalysis.sh, the first few steps (geneMrnacounts.py, normalizeExpandedExonic.py) go without any problems. However, geneMrnaCountsWeighted.py starts off fine but then starts pouring out errors, as shown below:


/proj/genome/commoncode3.0.1/geneMrnaCountsWeighted.py: version 3.7
dataset Sample.bowtie.rds
metadata:
bowtie_mapped True
dataType RNA
genome mm9
rdsVersion 1.1
readsize 36

9756706 unique reads, 1097314 spliced reads and 3706354 multireads
default cache size is 2000000 pages
found index

1 read 100000 read 200000 read 300000 read 400000 read 500000
10 read 600000 read 700000 read 800000 read 900000 read 1000000
11 read 1100000 read 1200000 read 1300000 read 1400000 read 1500000 read 1600000 read 1700000 read 1800000 read 1900000
12 read 2000000 read 2100000 read 2200000 read 2300000 read 2400000
13 read 2500000 read 2600000
14 read 2700000 read 2800000 read 2900000
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
15 read 3000000 read 3100000 read 3200000 read 3300000 gid 12419 not in gidReadDict
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
gid 12419 not in gidReadDict
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
gid 12419 not in gidReadDict
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
gid 12419 not in gidReadDict
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
gid 12419 not in gidReadDict
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
gid 12419 not in gidReadDict
Python(3391,0xa02bb720) malloc: *** mmap(size=100663296) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
gid 12419 not in gidReadDict


These go on for pages and pages, with different values for "gid" as it goes on.

Has anyone seen this problem? I can't figure out what I've done differently compared to my past successful runs. Any assistance would be MUCH appreciated.

Thanks!
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