[mira_talk] Re: Failure, wrapped MIRA process aborted
- From: "Mendez Garcia, Celia" <cmendezg@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 8 Jul 2014 17:01:00 +0000
Hi Bastien,
many thanks. You guys are great.
Everything worked perfectly fine.
I would like to ask you how you manage to assess quality to your assembly. I
was mapping against a reference, which of course helped, but then I found out
that my reference's quality, a closed genome and all that, is not as good as
one may have thought. Should I assemble de novo and then compare? How do you
differentiate among artifacts, missing data, etc. I attach a couple of info
.txt I got using from sub-sampled data.
Thanks..
Celia
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] on behalf
of Bastien Chevreux [bach@xxxxxxxxxxxx]
Sent: Wednesday, June 04, 2014 1:34 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Failure, wrapped MIRA process aborted
On 04 Jun 2014, at 18:37 , Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> […]
> Personally I would tell MIRA to ignore the long read names.
Or use “rename_prefix” in the manifest file to have on-the-fly renaming of
reads.
In your case
rename_prefix=HWI-ST330:422:C4AVHACXX clostraur
should do the trick.
In other news:
- mapping in draft mode is not that much faster than in accurate mode, I
recommend accurate.
- you are mapping almost 20m reads. If the reference is a bacterium, it’s
almost sure MIRA will tell you that this is not a good idea … and tell you what
to do :-)
B.
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Localtime: Tue Jun 10 16:32:10 2014
Assembly information:
=====================
Localtime: Tue Jun 10 16:32:10 2014
MIRA version: 4.0.2
Num. reads assembled: 325198
Num. singlets: 0
Coverage assessment (calculated from contigs >= 5000 with coverage >= 0):
=========================================================
Avg. total coverage: 8.33
Avg. coverage per sequencing technology
Sanger: 0.00
454: 0.00
IonTor: 0.00
PcBioHQ: 0.00
PcBioLQ: 0.00
Text: 3.00
Solexa: 5.33
Solid: 0.00
Large contigs (makes less sense for EST assemblies):
====================================================
With Contig size >= 500
AND (Total avg. Cov >= 3
OR Cov(san) >= 0
OR Cov(454) >= 0
OR Cov(ion) >= 0
OR Cov(pbh) >= 0
OR Cov(pbl) >= 0
OR Cov(txt) >= 1
OR Cov(sxa) >= 2
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 1
Total consensus: 6001982
Largest contig: 6001982
N50 contig size: 6001982
N90 contig size: 6001982
N95 contig size: 6001982
Coverage assessment:
--------------------
Max coverage (total): 1656
Max coverage per sequencing technology
Sanger: 0
454: 0
IonTor: 0
PcBioHQ: 0
PcBioLQ: 0
Text: 3
Solexa: 1653
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 38
Consensus bases with IUPAC: 17052 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 1407 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 109 (you might want to
check these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 1 (you might want to
check these)
All contigs:
============
Length assessment:
------------------
Number of contigs: 1
Total consensus: 6001982
Largest contig: 6001982
N50 contig size: 6001982
N90 contig size: 6001982
N95 contig size: 6001982
Coverage assessment:
--------------------
Max coverage (total): 1656
Max coverage per sequencing technology
Sanger: 0
454: 0
IonTor: 0
PcBioHQ: 0
PcBioLQ: 0
Text: 3
Solexa: 1653
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 38
Consensus bases with IUPAC: 17052 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 1407 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 109 (you might want to
check these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 1 (you might want to
check these)
Localtime: Tue Jul 1 04:20:09 2014
Assembly information:
=====================
Localtime: Tue Jul 1 04:20:09 2014
MIRA version: 4.0.2
Num. reads assembled: 865156
Num. singlets: 0
Coverage assessment (calculated from contigs >= 5000 with coverage >= 0):
=========================================================
Avg. total coverage: 17.22
Avg. coverage per sequencing technology
Sanger: 0.00
454: 0.00
IonTor: 0.00
PcBioHQ: 0.00
PcBioLQ: 0.00
Text: 3.00
Solexa: 14.22
Solid: 0.00
Large contigs (makes less sense for EST assemblies):
====================================================
With Contig size >= 500
AND (Total avg. Cov >= 6
OR Cov(san) >= 0
OR Cov(454) >= 0
OR Cov(ion) >= 0
OR Cov(pbh) >= 0
OR Cov(pbl) >= 0
OR Cov(txt) >= 1
OR Cov(sxa) >= 5
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 1
Total consensus: 6002288
Largest contig: 6002288
N50 contig size: 6002288
N90 contig size: 6002288
N95 contig size: 6002288
Coverage assessment:
--------------------
Max coverage (total): 4207
Max coverage per sequencing technology
Sanger: 0
454: 0
IonTor: 0
PcBioHQ: 0
PcBioLQ: 0
Text: 3
Solexa: 4204
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 42
Consensus bases with IUPAC: 14309 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 2374 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 167 (you might want to
check these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 1 (you might want to
check these)
All contigs:
============
Length assessment:
------------------
Number of contigs: 1
Total consensus: 6002288
Largest contig: 6002288
N50 contig size: 6002288
N90 contig size: 6002288
N95 contig size: 6002288
Coverage assessment:
--------------------
Max coverage (total): 4207
Max coverage per sequencing technology
Sanger: 0
454: 0
IonTor: 0
PcBioHQ: 0
PcBioLQ: 0
Text: 3
Solexa: 4204
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 42
Consensus bases with IUPAC: 14309 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 2374 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 167 (you might want to
check these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 1 (you might want to
check these)
Other related posts:
- » [mira_talk] Failure, wrapped MIRA process aborted- Gutierrez, Juan
- » [mira_talk] Re: Failure, wrapped MIRA process aborted- Bastien Chevreux
- » [mira_talk] Failure, wrapped MIRA process aborted- Mendez Garcia, Celia
- » [mira_talk] Re: Failure, wrapped MIRA process aborted- Peter Cock
- » [mira_talk] Re: Failure, wrapped MIRA process aborted- Bastien Chevreux
- » [mira_talk] Re: Failure, wrapped MIRA process aborted - Mendez Garcia, Celia
- » [mira_talk] Re: Failure, wrapped MIRA process aborted- Bastien Chevreux
- » [mira_talk] Failure, wrapped MIRA process aborted.- Mercedes Bigi
- » [mira_talk] Re: Failure, wrapped MIRA process aborted.- Bastien Chevreux
- » [mira_talk] Re: Failure, wrapped MIRA process aborted.- Mercedes Bigi
- » [mira_talk] Re: Failure, wrapped MIRA process aborted.- Bastien Chevreux
