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Bowtie2 alignment error

Hi,

I gave this simple command

bowtie2 -x /path/to/my/index -1 fastq1 -2 fastq2 -S output.sam

resultant:

Error: Encountered Internal Bowtiw 2 exception (#1)
Command: bowtie2 -x /path/to/my/index -1 fastq1 -2 fastq2 -S output.sam
(ERR): bowtie2-align exited with value 1

I have tried bowtie2-align as well with -l and -s switches. My index files are properly created with all 6 .bt2 files

Kindly help me sort this out.

Regards, Qurat

alignment next-gen bowtie2-align
• 5,318 views • link
written by micro32uvas • micro32uvas

You probably are but just to check: Are you using the correct basename for the index files?

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written by GenoMax GenoMax

I'd given the basename while indexing as "xyz_index". It created following files:

xyz_index.1.bt2 xyz_index.2.bt2 xyz_index.3.bt2 xyz_index.4.bt2 xyz_index.rev.1.bt2 xyz_index.rev.2.bt2

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written by micro32uvas • micro32uvas

What version of bowtie2 are you using? If it is not the latest then the first thing to try would be to upgrade. Has this index been successfully used before for other alignments?

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written by GenoMax GenoMax

I have been using the said version before. Its just that i completed the indexing a few hours back and tried the alignment but it wont let me move ahead.

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written by micro32uvas • micro32uvas

i did try bowtie2-align, where it would give the error about the -l or -s switch usage.

Using either one of them gives the error pertaining the warning that, "Bowtie 2-align was un directly. it is recommended that you run the wrapper script bowtie 1 instead"

but then using bowtie2 alone, still gives the error but in the above given manner.

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written by micro32uvas • micro32uvas

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

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written by GenoMax GenoMax

Try just one of the fastq files, perhaps one of them has an error.

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written by Devon Ryan Devon Ryan

1 answer

The main problem was in the .gz files. Bowtie2 doesnt take zip or gz files as a input.

Problem resolved. Thanks Devon Ryan and genomax2

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written by micro32uvas • micro32uvas

It doesn't take zip files, but it will take gzipped files.

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written by Devon Ryan Devon Ryan

I had zipped files and had to gunzip them all in order to make the command, workable

However, now there's this one paired end data that generated around 55GB data initially and then stopped with " bowtie2-align died with signal 6 (ABRT) (core dumped)" error. What could be the possible reason.

One thing that comes to me is the storage availability (which was running short in current drive but still the space of around 16gb was available)

Your help is appreciated.

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written by micro32uvas • micro32uvas

You'd need to run the command inside gdb to catch the error (or guess which of the abort()s in the code is causing this).

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written by Devon Ryan Devon Ryan

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