Excellent, could you post your fastq, how you created your indexes, and the small test FASTQ, so I can try to reproduce the behavior on my own machine?
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Thanks.
Here is how I converted the reference genome, indexed it and tried to make the alignment.
- converting genome
/mnt/fastfs/bin/bfast fasta2brg -A 1 -f refseq.fas
- INDEXING
qsub -q cb_quad -b y -e /mnt/fastfs/KW_Temp/bfast -o /mnt/fastfs/KW_Temp/bfast "/mnt/fastfs/bin/bfast index -f /mnt/fastfs/KW_Temp/bfast/refseq.fas -m <for each mask> -w 14 -A 1 -i <mask number>"
MASKS
M1 = 1111111111111111111111
M2 = 111110100111110011111111111
M3 = 10111111011001100011111000111111
M4 = 1111111100101111000001100011111011
M5 = 111111110001111110011111111
M6 = 11111011010011000011000110011111111
M7 = 1111111111110011101111111
M8 = 111011000011111111001111011111
M9 = 1111111111110011101111111
M10 = 1110110001011010011100101111101111
-ALIGNING:
qsub -q cb_quad -b y -e /mnt/fastfs/KW_Temp/bfast -o /mnt/fastfs/KW_Temp/bfast "/mnt/fastfs/bin/bfast match -f /mnt/fastfs/KW_Temp/bfast/refseq.fas -A 1 -r /mnt/fastfs/KW_Temp/input.fastq > /mnt/fastfs/KW_Temp/bfast/output.bmf"
I have done one test:
I extracted 5 seqs from fastq file and run test against this tiny file. It run without the problem.
It is really strange as using "-s 1 -e 5" options on full data set, so in fact providing the same sequences, causes the error reported earlier.
K
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Bfast Malloc memory error
Hi,
Has there been a solution to the Malloc memory error when running Bfast?
I am having the same problem when trying to run bfast bwaaln
bfast+bwa-0.7.0a/bfast/bfast bwaaln -n 0.04 -o 1 -e -1 -d 5 -i 5 -l 25 -k 2 -M 3 -t 8 -O 11 -E 4 -c -q 20 bfast_bwa_index/hg18_noran_mask.fa T3460_R3.fastq > bfast_matches_R3_bwa_T3460.bmf
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.80 sec
[bwa_aln_core] write to the disk... ************************************************************
In function "bwa_aln_core": Fatal Error[MallocMemory]. Message: Could not allocate (malloc) memory.
***** Exiting due to errors *****
I am running on Ubuntu with 32 Gb RAM.
Any help would be greatly appreciated
thanks alig
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Bfast Malloc memory error
Hi,
I tried with a hugely smaller dataset & didn't get the error. So then I tried with a different fastq file which I had run through a script to remove any entries which look broken and also had run through fastq_quality_filter. This also did not produce the error.
So I am hopeful that this was an issue with poor quality data.
Thanks
alig
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