Warning during normalize-by-median

[danbacastro]

Hello everybody,

I'm getting the following message during the normalize-by-median of my unpaired sequences:

** WARNING: hashsize is default! You absodefly want to increase this!
** Please read the docs!

My commands are listed below:

interleave-reads.py -o "metagen1.trimmed.interleaved.fastq metagen1.trimmed_R1.fastq / metagen1.trimmed_R2.fastq;
normalize-by-median.py -p -k 20 -C 20 -N 4 -x 10e9 -s normC20k20.kh *.interleaved.fastq;
normalize-by-median.py -C 20 -l normC20k20.kh -s normC20k20.kh *unpaired.fastq;

The first normalize-by-median runs without any warning, but the second displays that. The output looks right, should I be worried about it?

Thank you in advance,

Daniel

[ctb]

Hi Daniel,

thanks for the e-mail! This should be fixed in versions more recent than
March - what version of khmer are you using?

thanks,
--titus

On Mon, Aug 11, 2014 at 01:06:52PM -0700, danbacastro wrote:

Hello everybody,

I'm getting the following message during the normalize-by-median of my unpaired sequences:

** WARNING: hashsize is default! You absodefly want to increase this!
** Please read the docs!

My commands are listed below:

interleave-reads.py -o "metagen1.trimmed.interleaved.fastq metagen1.trimmed_R1.fastq / metagen1.trimmed_R2.fastq;
normalize-by-median.py -p -k 20 -C 20 -N 4 -x 10e9 -s normC20k20.kh *.interleaved.fastq;
normalize-by-median.py -C 20 -l normC20k20.kh -s normC20k20.kh *unpaired.fastq;

The first normalize-by-median runs without any warning, but the second displays that. The output looks right, should I be worried about it?

Thank you in advance,

Daniel

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Reply to this email directly or view it on GitHub:

#131

C. Titus Brown, ctb@msu.edu

[danbacastro]

Hi Dr Titus,

I'm using khmer 0.6.1. The output looks right, should I be worried about it?

Thanks

[ctb]

On Mon, Aug 11, 2014 at 01:30:37PM -0700, danbacastro wrote:

I'm using khmer 0.6.1. The output looks right, should I be worried about it?

No, khmer 0.6.1 works mostly OK, but you should upgrade to khmer 1.1 when
you can! We've made a LOT of changes, all in the (hopefully) positive
direction.

best,

--titus

C. Titus Brown, ctb@msu.edu

[danbacastro]

Thank you very much Titus,

I'll try to upgrade khmer.

Best Regards,

Daniel

[ctb]

Let us know how it goes -- should be mostly painless!

On Mon, Aug 11, 2014 at 01:33:49PM -0700, danbacastro wrote:

Thank you very much Titus,

I'll try to upgrade khmer.

Best Regards,

Daniel

---

Reply to this email directly or view it on GitHub:

#131 (comment)

C. Titus Brown, ctb@msu.edu