Open danbacastro opened 10 years ago
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
Reply to this email directly or view it on GitHub:
https://github.com/ged-lab/khmer-protocols/issues/131
C. Titus Brown, ctb@msu.edu
Hi Dr Titus,
I'm using khmer 0.6.1. The output looks right, should I be worried about it?
Thanks
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,
C. Titus Brown, ctb@msu.edu
Thank you very much Titus,
I'll try to upgrade khmer.
Best Regards,
Daniel
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:
https://github.com/ged-lab/khmer-protocols/issues/131#issuecomment-51836572
C. Titus Brown, ctb@msu.edu
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