Question

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

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7.7 years ago

micro32uvas ▴ 20

Hello,

I encounter an error while running the bowtie2 for genome mapping. After indexing I have generated the sam files for my other genomes. However, there is this one paired end sample, which generated more than 55GB of the SAM file and ended up with: Error while flushing and closing output (This was repeated for around 15times) terminate called after throwing an instance of 'int' bowtie2-align died with signal 6 (ABRT) (core dumped)

The sam file can still be opened and I can see the data in there, I assume that the data is not complete. And the file for the unaligned reads are still empty with noting in it.

I have checked the wc -l for both of the paired data set. Both files contain exact same number of reads. the Fastqc of both the files is also fine.

Anyone knows what is going on with my file data? Many thanks.

Qurat

bowtie2 genome mapping alignment • 15k views

ADD COMMENT • link 7.7 years ago by micro32uvas ▴ 20

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Could you reproduce the error with latest version of Bowtie2; which is your version?

Also check your disk space and RAM usage that they are not full at runtime.

ADD REPLY • link 7.7 years ago by Santosh Anand 5.8k

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Could you tell us the specifics of the machine (or HPC) you're running bowtie2 onto, and the file dimensions?

ADD REPLY • link 7.7 years ago by Matteo Schiavinato ★ 3.6k

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The system model is Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz Additionally I'v done alignment previously and it went pretty well. The current file with the said errors are of 40030292kb each.

ADD REPLY • link 7.7 years ago by micro32uvas ▴ 20

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I've just completed a whole job of around 40030292kb*18 files already with 24 threads and it worked just fine. I've even processed larger files than that. My query: Since rest of the paired files aligned quite easily and without any kind of error. Why suddenly Ram/ threading issue here in this last paired sample. P.S. RAM and other cores were available and it didnt show any malfunctioning.

ADD REPLY • link 7.7 years ago by micro32uvas ▴ 20

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Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLY • link 7.7 years ago by GenoMax 148k

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hi , do you get any satisfactory solution ? I also have encountered with similar problem, I used different version of bowtie2 (bowtei2 v. 2.2.2.9 , bowtie2 v. 2.2.3.4) as well but get same error. I have 96 GB of RAM and 5 TB HDD with intel xeon X5675 hexa core processors (redhat 6.2). I used 1 or 2 processor as well but result is same. The input fasta file is only 25 MB. any suggestions ?

ADD REPLY • link 6.9 years ago by drac2106 • 0

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Have you tried re-creating the genome index locally (if you were using a pre-made one)?

ADD REPLY • link 6.9 years ago by GenoMax 148k

score 0 · Answer 1 · 2017-05-08

Based on this discussion: https://lists.freebsd.org/pipermail/freebsd-questions/2004-April/042665.html

Signal 6 is SIGABRT -- see /usr/include/sys/signal.h. A process dying with this signal is usually due to it calling the abort(3) function. That generally indicates that the process itself has found that some essential pre-requisite for correct function is not available and voluntarily killing itself, rather than the process being killed by the kernel because it ran over resource limits or looked at memory addresses funny or something.

It seems that you're lacking of essential pre-requisites (my guess: RAM or number of cores to hold the multi-threading). Bowtie2 can be very demanding and is usually best run in an HPC than in a normal machine.

I don't think you can solve this problem unless you split your input files!