[mira_talk] Re: 0.5TB not enough space?
- From: Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Aug 2011 14:37:53 -0400
Dear Iddo,
There's another issue with your data: it looks noisy. Look at this
section of the log file:
Measured avg. frequency coverage: 1014
Deduced thresholds:
-------------------
Min normal cov: 405.6
Max normal cov: 1622.4
Repeat cov: 1926.6
Heavy cov: 8112.0
Crazy cov: 20280.0
Mask cov: 101400
Repeat ratio histogram:
-----------------------
0 5028189
1 837017
2 269532
3 37454
4 4716
The repeat ratio histogram of a clean sequence file from a genome
sequencing with decent coverage will show the "1" bin to be the biggest.
The fact that the 0 bin is biggest is a sign that your sequences are
filled with random sequence not from your bacteria. That's even more
true with such a high coverage.
Regards,
Bob
Bastien Chevreux wrote:
On Monday 15 August 2011 19:36:32 Iddo Friedberg wrote:
> Oops. I put up the wrong logfile. The run was definitely not on an NFS
> system
Heavens! Is there any valid reason you set up an assembly with a
coverage >= 1000x ? No, not ten, not one hundred ... one thousand! You
are aware that this actually decreases the quality of a genome
assembly, right? Non-random errors in the sequencing will be the death
of it.
You might want to read quickly through
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_seqadv_a_word_or_two_on_coverage
especially the small paragraph labelled with a nice, warm and
re-assuring "Warning".
Back to your project: slash down the amount of data by a factor of ten
and all will be well :-)
B.
PS: and I'm actually now thinking of adding another warning flag which
will let MIRA stop if it detects a coverage >= 150x in genome de-novo
... anyone having an oppinion on this?
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