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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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Old 09-09-2011, 08:37 AM   #2
nkwuji
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Default

It seems something is wrong with the compilation of the programs. After I recompile the programs using blimps following the instruction, most of the programs worked well (except choose_seqs_via_psiblastseedmedian).

However, the pre-compiled "fastaseqs" still gives "segmentation errors" occasionally. When I checked the compilation of "fastaseqs", it seems it is compiled using GNU 2.0.0, while my linux is GNU 2.10.0. There is no "fastaseqs" source code in the package. Is there any source code available for "fastaseqs"?

Cheers,
Jun
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Old 12-20-2011, 10:35 PM   #3
haishenruo
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Location: China

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Default

Hi,recently I have same problem like you,I don't know how to sove it.Have you figured out your problem ,can you give me some advice?The following is the problem I met:

./SIFT_for_submitting_fasta_seq -d $BLASTDB -f ../test/lacI.subst ../test/lacI.fasta > results.txt
Warning: lcl|Query_1 gi|2506562|sp|P03023|LACI_ECOLI LACTOSE OPERON REPRESSOR: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported with PSSMs, resetting to default value of standard composition-based statistics
./seqs_chosen_via_median_info: line 240: 14697 Segmentation fault psiblast_res_to_fasta_dbpairwise $QUERY.out $QUERY.globalX $ITERATIONS $QUERY.unfiltered
seqs_chosen_via_median_info: psiblast_res_to_fasta_dbpairwise failed.
SIFT_for_submitting_fasta_seq: seqs_chosen_via_median_info failed.
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