It appears that blat is trying to use 2.6G when only 0.5G is available. This requirement would be in-line with what human genome index will require in terms of RAM.
You have enough memory on your machine?
Assuming yes: Using 'ulimit -a' in a terminal will show you the restrictions on memory usage and you may be able to increase those. If not, you may want to talk to your sys admin.
Blat probably needs the fasta files when 2bit indexes are used for alignment. You should be able to regenerate the fasta files with the twoBitToFa command.
usage: blat database query [-ooc=11.ooc] output.psl where:
database and query are each either a .fa, .nib or .2bit file,
or a list of these files with one file name per line.
by default blat will produce PSL format output (tab delimited) if you need the output to be in some other format look at the options for -out command modifier.
-out=type Controls output file format. Type is one of:
psl - Default. Tab-separated format, no sequence
pslx - Tab-separated format with sequence
axt - blastz-associated axt format
maf - multiz-associated maf format
sim4 - similar to sim4 format
wublast - similar to wublast format
blast - similar to NCBI blast format
blast8- NCBI blast tabular format
blast9 - NCBI blast tabular format with comments
You can see help for blat by running the command without any options on the command line.
But still the same error after changing the position also :
./blat ucsc.hg19.fasta filtered_intron.txt -out=psl filtered_intron_blat.psl
Loaded 3137161264 letters in 93 sequences
Couldn't open chr1 , No such file or directory
Hmm. That is odd. What does your filtered_intron.txt file look like? I have a feeling that it is not in fasta (but probably BED) format.
$ head -5 filtered_intron.txt
Looks like your input file has variants/SNP's listed for specific positions? This file is NOT going to work with blat (which requires a simple fasta format file at a minimum). Are these SNP's from introns?
Can you provide additional clarification as to what you are trying to do?
Yes these are SNPs from introns. I am using BLAT to remap all reads supporting a variant to the genome. For it I am using SNPiR pipeline to know RNA-editing sites.
So how is it possible to change over to more memory .
As I also made some suggested changes in memalloc.c. But it didn't helped.
Thanks
Are you running this in a VM? How much memory do you have? It appears that the OS is reporting that there is a limit of 0.5G (per process?)
You have enough memory on your machine? Assuming yes: Using 'ulimit -a' in a terminal will show you the restrictions on memory usage and you may be able to increase those. If not, you may want to talk to your sys admin.