Comments (8)
Hi
This was most likely caused by there was not enough memory available. 1. How much data did you provide to mitoz? 2. How much memory does your server have?
from mitoz.
from mitoz.
from mitoz.
Hi
16G RAM is generously not enough, unless the input data is very small, for example, the test data in this GitHub project. If the input data is ca. 2Gb, you need about 60G ram at least. You may check the readme file for more details.
Thanks!
from mitoz.
from mitoz.
Hi Sridhar,
You may check out the 2.3 Memory on https://github.com/linzhi2013/MitoZ/
Hope this helps.
Cheers
Guanliang
from mitoz.
from mitoz.
Sorry, I am not getting this usage with less memory. Can you explain it how could i use MitoZ with less memory (16 G RAM).
…
On Mon, Feb 24, 2020 at 5:36 PM Guanliang MENG @.***> wrote: Hi Sridhar, You may check out the 2.3 Memory on https://github.com/linzhi2013/MitoZ/ Hope this helps. Cheers Guanliang — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AOKXR5YFI2NM5UNQINPSPODREOZ4NA5CNFSM4KMN6S32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMXRVGQ#issuecomment-590289562>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOKXR52NXJSCPMLCLTJ4GNDREOZ4NANCNFSM4KMN6S3Q .
-- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: +91-452-2458212 Fax: +91-452-2459873 Mobile: +91-9751648767 Web:http://www.genomicsmku.org/FAC%20PROF/srithar.html http://www.genomicsmku.org/FAC%20PROF/srithar.html ***************************************************
You can use BWA (https://github.com/lh3/bwa) to align your fastq reads again some closely related species (with relaxed parameters) and then extracted only the mapped reads with samtools (https://github.com/samtools/) output in fastq format.
then using the result fastq reads for mitogenome assembly.
now this method has been updated on https://github.com/linzhi2013/MitoZ/blob/master/version_2.4-alpha/README.md.
from mitoz.
Related Issues (20)
- Nanopore sequence for Mitochondrial genome assembly? HOT 4
- Is longer Illumina reads or shorter reads preferred? HOT 3
- mitoz visualize -h HOT 3
- 2 Mitogenomes in One Sample HOT 2
- Other animal taxa? HOT 3
- Error encountered in mt_assembly using mitoz all command HOT 2
- How to introduce breakpoints? HOT 1
- overlap_information file empty and mitogenomes not circularised HOT 1
- How to make cirular map to linear? HOT 1
- I got an error when I install the taxdump.tar.gz into sqlite3, why ? HOT 2
- Open Reading Frame HOT 1
- Missing genes with Udocker HOT 4
- mitoz3.4 annotations draw circle diagrams all have a gap, but in other annotation platforms are circular HOT 13
- Annotation of Gene on Both Sides of Start and End Position Got Cut Off HOT 1
- Can not find assembly_file: HOT 13
- Incorrect stop codon HOT 8
- Mitoz is not working in different directory HOT 12
- samtools in draw_circos_for_mitogenome_auto_depth.pl line 138 HOT 4
- All sequences are low abundance (<10X) -- RNA Seq data HOT 3
- makeblastdb error with MitoZ3.5 using Singularity HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from mitoz.