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Segmentation fault (core dumped)

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

segmentation-fault blat
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updated by Ram Ram • written by isha.lily20 • isha.lily20

1 answer

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

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written by Mensur Dlakic Mensur Dlakic

Hello sir

Can you give me solution for memory issue

Thank you

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written by isha.lily20 • isha.lily20

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?

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written by dsull dsull

Hello

I am running on my university server using BLAT

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

Thank you

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written by isha.lily20 • isha.lily20

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?)

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written by dsull dsull

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

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updated by Ram Ram • written by isha.lily20 • isha.lily20

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.

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written by GenoMax GenoMax

Thank you sir

I am now using high RAM, query solved :)

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written by isha.lily20 • isha.lily20

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