If you downloaded blat,
rather than compiling from source,
you would be limited to 32-bit and 4GB I think.
Recompiling from source on a 64-bit machine
would let you use plenty of ram.
-Galt
Hiram Clawson:
> Is your query sequence an unusual size ?
>
> To run per-chrom:
>
> $ twoBitInfo hg18.2bit stdout | cut -f1 | while read C
> do
> blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 -out=blast9 \
> hg18.2bit:${C} test_seq.txt test_seq_blas9.${C}.out
> done
>
> If you use the default output format of PSL you could then use the various
> psl* commands to filter the output.
>
> --Hiram
>
> Vinodh Srinivasasainagendra wrote:
>> Mine looks like:
>>
>> core file size (blocks, -c) 0
>> data seg size (kbytes, -d) unlimited
>> scheduling priority (-e) 0
>> file size (blocks, -f) unlimited
>> pending signals (-i) 139264
>> max locked memory (kbytes, -l) 32
>> max memory size (kbytes, -m) unlimited
>> open files (-n) 1024
>> pipe size (512 bytes, -p) 8
>> POSIX message queues (bytes, -q) 819200
>> real-time priority (-r) 0
>> stack size (kbytes, -s) 10240
>> cpu time (seconds, -t) unlimited
>> max user processes (-u) 139264
>> virtual memory (kbytes, -v) unlimited
>> file locks (-x) unlimited
>>
>>
>> Which of the above parameters should I bump up?
>>
>> How to run blat per chromosome basis?
>>
>> thanks
>> vinodh
> _______________________________________________
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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