Error in bowtie2

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7.5 years ago

whiteeagle115 ▴ 10

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 • 4.6k views

ADD COMMENT • link updated 2.4 years ago by sayema.khan ▴ 10 • written 7.5 years ago by whiteeagle115 ▴ 10

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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.

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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

ADD REPLY • link 2.4 years ago by sayema.khan ▴ 10

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

ADD REPLY • link 7.5 years ago by GenoMax 149k

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

ADD REPLY • link 7.5 years ago by ATpoint 86k

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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

ADD REPLY • link updated 7.5 years ago by h.mon 35k • written 7.5 years ago by whiteeagle115 ▴ 10

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I suppose by

16 Gb RAM and 2T of memory

you mean 16 Gb RAM and 2T of disk?

ADD REPLY • link 7.5 years ago by h.mon 35k

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