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Old 09-05-2011, 08:05 AM   #1
nkwuji
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Location: Dublin

Join Date: Mar 2010
Posts: 19
Default Segmentation fault in sift4.03

Hi,

I recently came across the sift program. As I need to predict the effect of non-synonymous SNP on protein, I chose to use the sift sequence search (http://sift.jcvi.org/www/SIFT_seq_submit2.html). Because I have more than 1200 SNPs to check, I need to use the local version of sift (http://sift.jcvi.org/www/sift4.0.3b.tar.gz).

However, I failed to run sift in my linux server. It gives a lot of "Segmentation fault". I tried it on different linux machines, the outputs are quite similiar. The "Segmentation fault" is usually given by "psiblast_res_to_fasta_dbpairwise" and "clump_output_alignedseq". And the most weird thing is, sometimes it gives "Segmentation fault" and sometimes not. In other words, sometimes, it can run the program successfully and gives reasonable result. But mostly, it is just stopped by "Segmentation fault" from a random program (e.g. psiblast_res_to_fasta_dbpairwise).

Could someone give me some help? Has anyone ran sift successfully in their local linux machine? Or, would you recommend some other programs predicting effect of ns SNPs?

BTW, I am running a perl program using LWP::UserAgent submitting requests through their website. However, it seems they have a daily limit of 80 SNPs. So it will finish next month if I keeps submitting all my SNPs...

Cheers,
Jun

Last edited by nkwuji; 09-05-2011 at 08:07 AM.
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