Question: Blastclust Gives Segmentation Fault
gravatar for kaustubh.patil
8.3 years ago by
kaustubh.patil0 wrote:


I want to use blastclust program from standard standalone blast installation. I tried to cluster 26 strains of E. Coli;

blastclust -i e_coli.fna -o outfile -p F -L .9 -b T -S 95

It gave the following output;

Jan 17, 2011 12:43 PM Start clustering of 26 queries
Segmentation fault

Then I tried it with some random lines deleted from some sequences (while keeping the same paameters) and it worked.

Any suggestions what could be wrong and how to fix it?

best regards

PS: please let me know and I will send you the files!

sequence clustering • 2.0k views
ADD COMMENTlink modified 7.1 years ago by Hamish3.1k • written 8.3 years ago by kaustubh.patil0

segfaults (which are memory access violations) are usually caused by compiling the wrong version for your platform (so, compiling the 64-bit version on a 32-bit platform is a common cause). However, this doesn't seem to explain the intermittent nature of your problem. Can you post the input file somewhere?

ADD REPLYlink written 8.3 years ago by Simon Cockell7.3k
gravatar for Hamish
7.2 years ago by
Hamish3.1k wrote:

From your description I am assuming that your 26 sequences are the complete genomes of 26 strains of E. coli. If this is the case then, memory usage is likely the cause of the problem. I guess you are using a pre-compiled distribution of BLAST download from NCBI, so as Simon suggests, check that the binaries you have downloaded match your system.

Since the memory requirements will be large I would recommend running this job on a 64-bit system and using the corresponding 64-bit binaries. Depending on the system configuration you may have to adjust the user memory limits using 'ulimit' or 'unlimit' before running 'blastclust' to ensure it can access all of the available resources.

ADD COMMENTlink written 7.2 years ago by Hamish3.1k
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