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.
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
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
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.
$ 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
************************************************************
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
*** glibc detected *** bfast: malloc():> memory corruption: 0x000000000220bcd0 **
Any ideas on how to solve this problem?
Thanks
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