Hello,
I'm attempting to align 30 million paired-end reads to hg19 from a 50-cycle illumina run with bowtie2.
I'm doing this one a computer with 12 cores and 48 GB ram.
I also get this error when using -p 4
The sam files are getting up to ~ 7 GB in size before it throws that error and stops. Based on comparing the last alignment names in the sam and the fastqs, it's getting about halfway through the fastq.
Am I running out of memory? When I check my free memory during alignment, it doesn't appear that I'm coming close to running out.
What can I do to get this to complete?
I'm attempting to align 30 million paired-end reads to hg19 from a 50-cycle illumina run with bowtie2.
I'm doing this one a computer with 12 cores and 48 GB ram.
Code:
[user@host folder]$ bowtie2 --dovetail -x /hg19/bt2_index/hg19 -1 219_0h_R1_val_1.fq -2 219_0h_R2_val_2.fq -p 12 -S 219_0h.sam terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc
The sam files are getting up to ~ 7 GB in size before it throws that error and stops. Based on comparing the last alignment names in the sam and the fastqs, it's getting about halfway through the fastq.
Am I running out of memory? When I check my free memory during alignment, it doesn't appear that I'm coming close to running out.
Code:
[user@host folder]$ free -g total used free shared buffers cached Mem: 47 12 34 0 0 6 -/+ buffers/cache: 6 41 Swap: 0 0 0
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