Question: problem in running cutadapt on multiple cores
0
gravatar for Javad
12 months ago by
Javad60
Javad60 wrote:

Dear all,

I am trying to use cutadadpt for trimming adapters. It works perfectly when I run it on single core but when I try to use it on multiple cores I get the following error.

ERROR: Traceback (most recent call last):
  File "/home/user/.local/lib/python3.6/site-packages/cutadapt/pipeline.py", line 445, in run
    output.buffer.name = self._orig_outfiles.out.name
AttributeError: 'BZ2File' object has no attribute 'name'

Traceback (most recent call last):
  File "/usr/local/bin/cutadapt", line 11, in <module>
    sys.exit(main())
  File "/home/user/.local/lib/python3.6/site-packages/cutadapt/__main__.py", line 747, in main
    stats = runner.run()
  File "/home/use/.local/lib/python3.6/site-packages/cutadapt/pipeline.py", line 637, in run
    raise e
AttributeError: 'BZ2File' object has no attribute 'name'

I would really appreciate any suggestions.

Thanks

rna-seq • 536 views
ADD COMMENTlink written 12 months ago by Javad60
1

It looks like multithreaded trimming only works for gzipped files at the moment. I would suggest that you post a bug report on github, since perhaps the authors can simply program around this.

ADD REPLYlink written 12 months ago by Devon Ryan90k

Can you share the 2 commands you’re using?

ADD REPLYlink written 12 months ago by jrj.healey12k

Hello,

Here it is:

This one works:

cutadapt -u 15 -U 5 -m 20 -g GATGGTTGAGGATGTGTGGAG -G GATGGTTGAGGATGTGTGGAG -g TCCACACATCCTCAACCATC -G CTCCACACATCCTCAACCATC -q 25 -o out_R1.fq.bz2 -p out_R2.fq.bz2 /path/to/file/input_R1.fq.bz2 /path/to/file/input_R2.fq.bz2

and this one doesn't:

cutadapt -j 40 -u 15 -U 5 -m 20 -g GATGGTTGAGGATGTGTGGAG -G GATGGTTGAGGATGTGTGGAG -g TCCACACATCCTCAACCATC -G CTCCACACATCCTCAACCATC -q 25 -o out_R1.fq.bz2 -p out_R2.fq.bz2 /path/to/file/input_R1.fq.bz2 /path/to/file/input_R2.fq.bz2

python --version
Python 3.6.4 :: Anaconda, Inc.

cutadapt --version
1.16
ADD REPLYlink written 12 months ago by Javad60

How many cpu threads are available to you? Do you really have 40?

Ensure you’re following all the suggestions here:

http://cutadapt.readthedocs.io/en/stable/guide.html#multi-core-support

ADD REPLYlink modified 12 months ago • written 12 months ago by jrj.healey12k

Yes. I have 40 cores.

ADD REPLYlink written 12 months ago by Javad60

What happens if you try it with, more than 1 but less than 40? Same error?

ADD REPLYlink written 12 months ago by jrj.healey12k
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