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Old 09-17-2010, 11:52 AM   #1
Location: St. Paul, MN

Join Date: Aug 2010
Posts: 34
Default BFAST memory error in postprocess

Hello, I have a set of 85-bp long solexa reads and I have already used BFAST match, local align, an postprocess (with -a 3 option) successfully.

I am now trying to filter the multi reads using the -a 4 option and am getting a memory error message.

This is the command I am using:

/bfast postprocess -f /filepath/TAIR9_chr_all.fas -i /filepath/bfast.aligned.split1_1_ZT0.baf -a 4 -O 1 > /filepath/bfast.reported.split1_1_ZT0.sam

This is the error message I am getting:

Checking input parameters supplied by the user ...
Validating fastaFileName /filepath/TAIR9_chr_all.fas.
Validating alignFileName /filepath/bfast.aligned.split1.baf.
Input arguments look good!
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /filepath/TAIR9_chr_all.fas
alignFileName: /filepath/bfast.aligned.split1.baf
algorithm: [Best Score All]
space: [NT Space]
unpaired: [Not Using]
reversePaired: [Not Using]
avgMismatchQuality: 10
scoringMatrixFileName: [Not Using]
randomBest: [Not Using]
minMappingQuality: -2147483648
minNormalizedScore: -2147483648
pairingStandardDeviation: 2.000000
gappedPairingRescue [Not Using]
numThreads: 1
queueLength: 50000
outputFormat: [SAM]
outputID: [Not Using]
RGFileName: [Not Using]
timing: [Not Using]
Reading in reference genome from /filepath/TAIR9_chr_all.fas.nt.brg.
In total read 7 contigs for a total of 119667750 bases
In function "AlignedEntryRead": Fatal Error[MallocMemory]. Variable/Value: a->alnRead.
Message: Could not allocate memory.
***** Exiting due to errors *****

This is the message I am getting with just this specific file. With other split file I am getting the message "line 3: 1182 Segmentation fault" (although the line is different depending on the file)

I cannot figure out what this means and would appreciate any advice!


Last edited by Marisa_Miller; 09-17-2010 at 11:58 AM.
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Old 09-17-2010, 12:09 PM   #2
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Try posting a test case to the bfast help mailing list ( I would be happy to help over there.
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Old 09-17-2010, 03:22 PM   #3
Location: St. Paul, MN

Join Date: Aug 2010
Posts: 34

I am not sure if this could be the problem, but it may be that I did all the other processing with version d and I am now using version e for the step in my above post? I will try doing everything with the new version for just one of my 12 libraries to see if it works.
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Old 09-18-2010, 05:35 AM   #4
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It could be. Use definitely the latest version. If you still have the problem send over some data so the bug can be track down.
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