Hello all,
I am using bwa mem to align contigs to a reference genome and I observed that it is exiting with an error message "Segmentation Fault". For example:
[M::main_mem] read 1 sequences (405327 bp)...
Segmentation fault
Upon closer examination, I found that whenever the size of input sequence >=0.4 Mbp, I see this message. In bwa mem page (http://bio-bwa.sourceforge.net/bwa.shtml), it is mentioned that it can handle contigs upto 1Mbp. I am unable to figure out the source of this upper limit at 0.4Mbp. Is it specific to my computer or is there any parameter by which I can assign more memory to bwa?
I am currently thinking of breaking contigs greater than 0.4Mbp into overlapping smaller contigs of size 399999. Is there any other way to go about it.
Thanks all,
Ramya
I am using bwa mem to align contigs to a reference genome and I observed that it is exiting with an error message "Segmentation Fault". For example:
[M::main_mem] read 1 sequences (405327 bp)...
Segmentation fault
Upon closer examination, I found that whenever the size of input sequence >=0.4 Mbp, I see this message. In bwa mem page (http://bio-bwa.sourceforge.net/bwa.shtml), it is mentioned that it can handle contigs upto 1Mbp. I am unable to figure out the source of this upper limit at 0.4Mbp. Is it specific to my computer or is there any parameter by which I can assign more memory to bwa?
I am currently thinking of breaking contigs greater than 0.4Mbp into overlapping smaller contigs of size 399999. Is there any other way to go about it.
Thanks all,
Ramya
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