Question: abyss-pe reading files endlessly with se command added
0
gravatar for pepijn.kooij
3.1 years ago by
Royal Botanic Gardens, Kew
pepijn.kooij0 wrote:

I'm running a abyss-pe job using trimmed paired-end MiSeq data of sample with appr. genome size of 120Mb. I trimmed my data using Trimmomatic, which gives 4 output files from the 2 original input files: 2 files are paired sequences (forward and reverse) and 2 files are unpaired sequences (forward and reverse).

I've been having problems with assembling the 4 files, it seems that abyss keeps reading the files endlessly without finishing.

The code I use is:

abyss-pe k=11 np=8 -C directory/for/my/output name=name_of_my_output lib='lib1' lib1='/path/to/forward_paired_trimmed.fastq.gz /path/to/reverse_paired_trimmed.fastq.gz' se='/path/to/forward_unpaired_trimmed.fastq.gz /path/to/reverse_unpaired_trimmed.fastq.gz'

I've also tried the following with the same result:

abyss-pe k=11 np=8 -C directory/for/my/output name=name_of_my_output in='/path/to/forward_paired_trimmed.fastq.gz /path/to/reverse_paired_trimmed.fastq.gz' se='/path/to/forward_unpaired_trimmed.fastq.gz /path/to/reverse_unpaired_trimmed.fastq.gz'

However, when I run the analysis with out the 'se' command it finishes reading the reads in appr. 30 min.:

abyss-pe k=11 np=8 -C directory/for/my/output name=name_of_my_output in='/path/to/forward_paired_trimmed.fastq.gz /path/to/reverse_paired_trimmed.fastq.gz'

Any idea why abyss has problems reading in the files when I add the 'se' command?

Please let me know if more information is needed.

EDIT: I'm using the latest abyss version 1.9.0

EDIT 2: abyss-pe has now been running for 1250 mins, and still reading in the files, I have -v=vv on, screen shot of the verbose shows this:

extra verbose of abyss-pe run

abyss miseq paired-end assembly • 1.6k views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 3.1 years ago by pepijn.kooij0
0
gravatar for mastal511
3.1 years ago by
mastal5112.0k
mastal5112.0k wrote:

Your commands look OK, the abyss-pe documentation does say that se data would considerably slow down the abyss-fixmate stage.

https://github.com/bcgsc/abyss#assembling-a-paired-end-library

ADD COMMENTlink written 3.1 years ago by mastal5112.0k

Yes, I read that, but it's not even getting to that point. It just 'hangs' at reading in the files. I had one analysis turned on on Friday, and it was still reading the files this morning (Monday). I killed the process to play around with the settings and try to figure out what the issue is, without success

ADD REPLYlink written 3.1 years ago by pepijn.kooij0
0
gravatar for pepijn.kooij
3.1 years ago by
Royal Botanic Gardens, Kew
pepijn.kooij0 wrote:

Ok, I figured what was happening, but still confused.

I previously had abyss deployed with a maxk set at 256, redeploying it with maxk set at 96 did the trick. The strange thing is that the abyss github readme.md says this:

The default maximum k-mer size is 64 and may be decreased to reduce memory usage or increased at compile time. This value must be a multiple of 32 (i.e. 32, 64, 96, 128, etc):

./configure --enable-maxk=96

From that I would assume any multitude of 32 should be possible, but apparently it's not. Anyone has any idea what the real maximum maxk setting is?

ADD COMMENTlink written 3.1 years ago by pepijn.kooij0
0
gravatar for mastal511
3.1 years ago by
mastal5112.0k
mastal5112.0k wrote:

See this discussion of the problem in a previous thread:

ABySS assembly runs forever

ADD COMMENTlink written 3.1 years ago by mastal5112.0k

Thanks, I'll try to add those export open-mpi lines to my script to see if that helps with larger maxk values and will post the results here.

ADD REPLYlink written 3.1 years ago by pepijn.kooij0
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