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Published 20 hours ago • verified publisher icon marbl

How to use meryl

Open Kalpi-ds opened this issue 4 years ago • 7 comments

Hi,

I have a fasta file which I wish to turn into kmers using meryl software. I have meryl version 1.0 installed in hpc. I followed this guide http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_Meryl

following is the command I used.

module load meryl meryl -P -m 21 -s file_name.fasta

I get the following message: Don't know what to do with '-m'. Don't know what to do with '21'. Don't know what to do with '-s'. Don't know what to do with 'file_name.fasta'

I appreciate if you can guide me on how to run meryl.

Thank you

Kalpi-ds avatar Sep 10 '20 02:09 Kalpi-ds

Hello,

The doc you are referencing is very old. Type meryl and see the help message.

In your example, counting kmers with:

meryl count k=21 file_name.fasta output file_name.meryl

arangrhie avatar Sep 10 '20 02:09 arangrhie

Thank you very much for the quick response. Now it is working fine. Where can I find the updated documentation.

Kalpi-ds avatar Sep 10 '20 03:09 Kalpi-ds

Hi @arangrhie

I have a list of files like following in the .meryl folder. Is this how the normal output looks like? or does it produce one .merylData file and one .merylIndex file when correctly executed?

0x000000.merylData 0x001001.merylIndex 0x010011.merylData 0x011100.merylIndex 0x100110.merylData 0x101111.merylIndex 0x111001.merylData 0x000000.merylIndex 0x001010.merylData 0x010011.merylIndex 0x011101.merylData 0x100110.merylIndex 0x110000.merylData 0x111001.merylIndex 0x000001.merylData 0x001010.merylIndex 0x010100.merylData 0x011101.merylIndex 0x100111.merylData 0x110000.merylIndex 0x111010.merylData 0x000001.merylIndex 0x001011.merylData 0x010100.merylIndex 0x011110.merylData 0x100111.merylIndex 0x110001.merylData 0x111010.merylIndex 0x000010.merylData 0x001011.merylIndex 0x010101.merylData 0x011110.merylIndex 0x101000.merylData 0x110001.merylIndex 0x111011.merylData 0x000010.merylIndex 0x001100.merylData 0x010101.merylIndex 0x011111.merylData 0x101000.merylIndex 0x110010.merylData 0x111011.merylIndex 0x000011.merylData 0x001100.merylIndex 0x010110.merylData 0x011111.merylIndex 0x101001.merylData 0x110010.merylIndex 0x111100.merylData 0x000011.merylIndex 0x001101.merylData 0x010110.merylIndex 0x100000.merylData 0x101001.merylIndex 0x110011.merylData 0x111100.merylIndex 0x000100.merylData 0x001101.merylIndex 0x010111.merylData 0x100000.merylIndex 0x101010.merylData 0x110011.merylIndex 0x111101.merylData 0x000100.merylIndex 0x001110.merylData 0x010111.merylIndex 0x100001.merylData 0x101010.merylIndex 0x110100.merylData 0x111101.merylIndex 0x000101.merylData 0x001110.merylIndex 0x011000.merylData 0x100001.merylIndex 0x101011.merylData 0x110100.merylIndex 0x111110.merylData 0x000101.merylIndex 0x001111.merylData 0x011000.merylIndex 0x100010.merylData 0x101011.merylIndex 0x110101.merylData 0x111110.merylIndex 0x000110.merylData 0x001111.merylIndex 0x011001.merylData 0x100010.merylIndex 0x101100.merylData 0x110101.merylIndex 0x111111.merylData 0x000110.merylIndex 0x010000.merylData 0x011001.merylIndex 0x100011.merylData 0x101100.merylIndex 0x110110.merylData 0x111111.merylIndex 0x000111.merylData 0x010000.merylIndex 0x011010.merylData 0x100011.merylIndex 0x101101.merylData 0x110110.merylIndex merylIndex 0x000111.merylIndex 0x010001.merylData 0x011010.merylIndex 0x100100.merylData 0x101101.merylIndex 0x110111.merylData 0x001000.merylData 0x010001.merylIndex 0x011011.merylData 0x100100.merylIndex 0x101110.merylData 0x110111.merylIndex 0x001000.merylIndex 0x010010.merylData 0x011011.merylIndex 0x100101.merylData 0x101110.merylIndex 0x111000.merylData 0x001001.merylData 0x010010.merylIndex 0x011100.merylData 0x100101.merylIndex 0x101111.merylData 0x111000.merylIndex

Kalpi-ds avatar Sep 10 '20 21:09 Kalpi-ds

Yes, this is the expected meryl db output. It is a 'directory'. Just type meryl and read the help message. If anything is unclear, let us know.

arangrhie avatar Sep 16 '20 12:09 arangrhie

Dear author

I saw trio bin article, Use meryl to discover specific kmer,as follow image I'd like to ask what parameters I should use if I take the same part of the intersection I didn't see the details

duhuipeng avatar Jan 20 '21 06:01 duhuipeng

Hello, the meryl version used in the trio binning paper is a bit outdated.

The equivalent parameters with meryl1.0 release ~ recent version on the master is:

meryl difference k12.meryl o157.meryl output k12.only.meryl
meryl difference o157.meryl k12.meryl output o157.only.meryl

arangrhie avatar Feb 20 '21 02:02 arangrhie

Hi, I saw trio binning Scripts, following is the command I used.

../meryl/*/bin/meryl -Dt -n 25 -s k12.only

but it doesn't work, I'd like to ask what parameters I should use. Thank you

hlxie avatar Apr 27 '21 05:04 hlxie