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Old 09-26-2012, 11:57 AM   #1
flobpf
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Location: USA

Join Date: Apr 2010
Posts: 76
Question BFAST match error

Hi,

I'm getting the following error from BFAST with my colorspace SOLiD reads in FASTQ format. Couldn't figure out what it is...

All my reads are >20bp and I'm using a subset of all reads to test the program here.
Quote:
$ bfast match -f Mus_musculus.GRCm38.68.dna_rm.toplevel.fa -r ../test.fastq -A 1
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName Mus_musculus.GRCm38.68.dna_rm.toplevel.fa.
Validating readsFileName ../test.fastq.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: Mus_musculus.GRCm38.68.dna_rm.toplevel.f
a
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: ../test.fastq
offsets: [Using All]
loadAllIndexes: [Not Using]
compression: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
keyMissFraction: 1.000000
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 250000
tmpDir: ./
timing: [Not Using]
************************************************************
Searching for main indexes...
Found 1 index (4 total files).
Not using secondary indexes.
************************************************************
Reading in reference genome from Mus_musculus.GRCm38.68.dna_rm.toplevel.fa.cs.br
g.
In total read 66 contigs for a total of 2730871774 bases
************************************************************
Reading ../test.fastq into a temp file.
Will process 250 reads.
************************************************************
Searching index file 1/4 (index #1, bin #1)...
Reading index from Mus_musculus.GRCm38.68.dna_rm.toplevel.fa.cs.1.1.bif.
bfast: ../bfast/RGIndex.c:2015: RGIndexReadHeader: Assertion `index->length > 0'
failed.
▒ ♥Aborted
Thought this might be due to me giving BFAST an incomplete dataset. However, if I use the entire dataset (all FASTQ SOLiD reads), I get the following error
Quote:
*** glibc detected *** bfast: malloc():> memory corruption: 0x000000000220bcd0 **
which seems like BFAST is running out of usable memory, when, in fact, I'm specifying 20gb of memory for a one lane of SOLiD FASTQ reads.

Any ideas on how to solve this problem?

Thanks
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