Segmentation fault (core dumped)

Question

[isha.lily20]

Hello,

Can any one give me suggestions on Segmentation fault (core dumped) while doing BLAT (BLAST-LIke Alignment Tool) for pair wise sequence alignment, however the query size has no problem, but the reference genome size is bigger of saffron.

Thank you

Answer 1

[Mensur Dlakic]

It is usually a memory issue. You have not given us enough information to really help you.

[isha.lily20]

Hello sir

Can you give me solution for memory issue

Thank you

[dsull]

Hi! As was mentioned, you haven’t given us enough information to help you. Therefore we cannot give you a solution.

How/where exactly were you running BLAST?

[isha.lily20]

Hello

I am running on my university server using BLAT

Can you tell what kind of more information i have to give

Thank you

[dsull]

Are you typing a command to run it? What command are you typing?

People typically run BLAST via https://blast.ncbi.nlm.nih.gov/Blast.cgi -- but there are command-line versions that exist so which command-line BLAST program are you running (and what command are you running?)

[isha.lily20]

Hello sir

I am using this command line exactly given below:

blat -t=dna crocus_sativus.fasta2 -q=rna saffron-seq.fa -minScore=1 -out=psl output.psl

Thank you

[GenoMax]

How much RAM do you have? What is size of crocus file? If you don't have enough RAM available then there is no effective solution but to find alternate hardware or program to use.

That said -q=rna makes sense? If you are sequencing cDNA made from RNA then use DNA for both. If you have high throughput sequence data then use a proper NGS aligner instead of blat.

[isha.lily20]

Thank you sir

I am now using high RAM, query solved :)