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Error in bowtie2

Hello,

I just have a problem using bowtie2 (with paired-end files), and I don't know where to start to correct.

Error while flushing and closing output terminate called after throwing an instance of 'int'

(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

I just compared the amount of the reads in the files and it's the same.

Thanks!

bowtie2 genome mapping
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updated by sayema.khan • sayema.khan • written by whiteeagle115 • whiteeagle115

Was there not enough room to complete writing results of the alignments to disk?

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written by GenoMax GenoMax

Have you checked the suggestions and solutions in this thread on SeqAnswers? A good first reflex is to google your error message. If you are using a common tool (such as bowtie2) the chance is big that someone else already came across the same issue.

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written by WouterDeCoster WouterDeCoster

Signal 6 often indicates a memory issue. Please provide the full command and the specs of the machine you use.

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written by ATpoint ATpoint

Thanks for all the answers! I'm using a server with 16 Gb RAM and 2T of memory. The command line: 

bowtie2  -x SalI -1 121_MSO_1.fastq -2 121_MSO_2.fastq -p 20 -D 20 -R 3 -N 1 -L 20 -i S,1,0.5 -S 121_unt.sam
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updated by h.mon h.mon • written by whiteeagle115 • whiteeagle115

I suppose by

16 Gb RAM and 2T of memory

you mean 16 Gb RAM and 2T of disk?

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written by h.mon h.mon

Did you find a solution for this? I am having the same issue..

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written by sayema.khan • sayema.khan

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