Hi
I have been using BFAST successfully for ABI alignment to hg18 for a while now. I have fresh installs of versions 0.6.1c, 0.6.3c and the latest 0.6.4e. Each version is make by
sh autogen.sh
./configure
make
Depending which I point PATH to I find that the first two work fine under Mac OS 10.5.8 on a lowly Duocore/4Gb machine, but the most recent version falls over when making a reference index from an exons files.
So
bfast index -f hg18all.fa -A 1 -n 2 -m 1111111111111111111111 -w 14 -t -i 1 -x exonFile.txt -T /tmp/
... runs fine for the first two versions, but with 0.6.4e gives a malloc error (terminal output pasted below). Interestingly, the 0.6.4e version does run successfully on my Snow Leopard laptop, suggesting some sensitivity to the background OS.
Best regards
David
=========
dk$ bfast index -f $hg18dir/hg18all.fa -A 1 -n 2 -m 1111111111111111111111 -w 14 -t -i 1 -x $exondir/pan73regions.txt -T /tmp/
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /Users/dk/Desktop/pan/data/hg18Genome/hg18all.fa.
Validating exonsFileName /Users/dk/Desktop/pan/documentation/pan73regions.txt.
Validating tmpDir path /tmp/.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /Users/dk/Desktop/pan/data/hg18Genome/hg18all.fa
space: [Color Space]
mask: 1111111111111111111111
depth: 0
hashWidth: 14
indexNumber: 1
repeatMasker: [Not Using]
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: /Users/dk/Desktop/pan/documentation/pan73regions.txt
numThreads: 2
tmpDir: /tmp/
timing: [Using]
************************************************************
Reading in exons from /Users/dk/Desktop/pan/documentation/pan73regions.txt.
Read in 73 exons.
************************************************************
Reading in reference genome from /Users/dk/Desktop/pan/data/hg18Genome/hg18all.fa.cs.brg.
In total read 24 contigs for a total of 3080419480 bases
************************************************************
Creating the index...
************************************************************
Warning: startContig was less than zero.
Defaulting to contig=1 and position=1.
************************************************************
************************************************************
Warning: endContig was greater than the number of contigs in the reference genome.
Defaulting to reference genome's end contig=24 and position=57772954.
************************************************************
Currently on [contig,pos]:
[------24,---57772954]
Sorting by thread...
Merging sorts from threads...
Out of 1 required merges, currently on:
1
Merge complete.
Sorted.
bfast(20212,0xa00e8720) malloc: *** mmap(size=1073741824) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
************************************************************
In function "RGIndexCreateHash": Fatal Error[MallocMemory]. Variable/Value: index->starts.
Message: Could not allocate memory.
***** Exiting due to errors *****
************************************************************
I have been using BFAST successfully for ABI alignment to hg18 for a while now. I have fresh installs of versions 0.6.1c, 0.6.3c and the latest 0.6.4e. Each version is make by
sh autogen.sh
./configure
make
Depending which I point PATH to I find that the first two work fine under Mac OS 10.5.8 on a lowly Duocore/4Gb machine, but the most recent version falls over when making a reference index from an exons files.
So
bfast index -f hg18all.fa -A 1 -n 2 -m 1111111111111111111111 -w 14 -t -i 1 -x exonFile.txt -T /tmp/
... runs fine for the first two versions, but with 0.6.4e gives a malloc error (terminal output pasted below). Interestingly, the 0.6.4e version does run successfully on my Snow Leopard laptop, suggesting some sensitivity to the background OS.
Best regards
David
=========
dk$ bfast index -f $hg18dir/hg18all.fa -A 1 -n 2 -m 1111111111111111111111 -w 14 -t -i 1 -x $exondir/pan73regions.txt -T /tmp/
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /Users/dk/Desktop/pan/data/hg18Genome/hg18all.fa.
Validating exonsFileName /Users/dk/Desktop/pan/documentation/pan73regions.txt.
Validating tmpDir path /tmp/.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /Users/dk/Desktop/pan/data/hg18Genome/hg18all.fa
space: [Color Space]
mask: 1111111111111111111111
depth: 0
hashWidth: 14
indexNumber: 1
repeatMasker: [Not Using]
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: /Users/dk/Desktop/pan/documentation/pan73regions.txt
numThreads: 2
tmpDir: /tmp/
timing: [Using]
************************************************************
Reading in exons from /Users/dk/Desktop/pan/documentation/pan73regions.txt.
Read in 73 exons.
************************************************************
Reading in reference genome from /Users/dk/Desktop/pan/data/hg18Genome/hg18all.fa.cs.brg.
In total read 24 contigs for a total of 3080419480 bases
************************************************************
Creating the index...
************************************************************
Warning: startContig was less than zero.
Defaulting to contig=1 and position=1.
************************************************************
************************************************************
Warning: endContig was greater than the number of contigs in the reference genome.
Defaulting to reference genome's end contig=24 and position=57772954.
************************************************************
Currently on [contig,pos]:
[------24,---57772954]
Sorting by thread...
Merging sorts from threads...
Out of 1 required merges, currently on:
1
Merge complete.
Sorted.
bfast(20212,0xa00e8720) malloc: *** mmap(size=1073741824) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
************************************************************
In function "RGIndexCreateHash": Fatal Error[MallocMemory]. Variable/Value: index->starts.
Message: Could not allocate memory.
***** Exiting due to errors *****
************************************************************
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