Question: Bowtie2 alignment error
0
gravatar for micro32uvas
2.3 years ago by
micro32uvas10
Pakistan
micro32uvas10 wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by micro32uvas10

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax70k

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

ADD REPLYlink written 2.3 years ago by micro32uvas10

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?

ADD REPLYlink written 2.3 years ago by genomax70k

Its bowtie2-align-s version 2.2.6

ADD REPLYlink written 2.3 years ago by micro32uvas10

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.

ADD REPLYlink written 2.3 years ago by micro32uvas10

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.

ADD REPLYlink written 2.3 years ago by micro32uvas10

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

ADD REPLYlink written 2.3 years ago by genomax70k

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

ADD REPLYlink written 2.3 years ago by Devon Ryan91k
1
gravatar for micro32uvas
2.3 years ago by
micro32uvas10
Pakistan
micro32uvas10 wrote:

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

ADD COMMENTlink written 2.3 years ago by micro32uvas10

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

ADD REPLYlink written 2.3 years ago by Devon Ryan91k

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.

ADD REPLYlink written 2.3 years ago by micro32uvas10

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).

ADD REPLYlink written 2.3 years ago by Devon Ryan91k
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