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local GENSCAN: error running - (Aug/31/2006 )

Hi ppl,

I have installed GENSCAN locally, and did not have any problem running it on the sample sequence file that came along with local GENSCAN package.

However, when i tried it with another genome file , an error showed up and the program stopped at that point of error.

Below is the sequence of command that i input, followed by the error message that showed up.

# genscan <parameter file path> <genomefilepath>

reading sequence file <genomefilepath> ........................"x" bp

reading parameter file <parameter file path> ................."y" matrices

scoring sequence............

Error: calloc failed on CUM_SCORE array.

Any idea as to what that error means and how it can be fixed up.???

-kamesh-

hi all, I found out that my local GENSCAN would not accept files, larger than 2MB. Hence it failed on the previous occasions, some of the common error messages i understand that arise when sequence input is larger than what GENSCAN can handles is as follows....

1. Error: calloc failed on CUM_SCORE array

2. reading sequence file HUMRASH... 'x' bp

reading parameter file /usr/lib/GENSCAN/HumanIso.smat... 14 matrices

scoring sequence... done

running Viterbi/forward algorithms... terminated/killed.....

BTY, I have since split the sequence input file (150MB - which is a whole genome in my case), into 75* 2MB files....and a GENSCAN on each of these files worked. However, one problem that arises out of this is that genes that lie midway at the split lines among the files, may not throw up when a GENSCAN is done.....I understand that GENSCAN of whole genomes are a routine....But how is such a problem overcome??/

any help in this regard will be greatly appreciated....

thanks a lot in advance..

-kamesh-