Comments (5)
mnshgl0110
commented on August 13, 2024
Hi. It seems that there are two issues. First is that the program is crashing. And second is that too few SNPs were identified.
The first issue seems to be a bug. Can you please share the log file so that I could have more information about the run?
For the second issue, can you please check how many SNPs are identified when using the show-snps utility from MUMmer? SyRI can only report SNPs which are identified by the MUMmer alignments. So, it would be worthwhile to first check whether are indeed SNPs present in the alignments or not. Additionally, please also upload the snps_GARB.txt file.
from syri.
liufuyan2016
commented on August 13, 2024
show-snps produce 17107349。 The syri.log is blank.
from syri.
liufuyan2016
commented on August 13, 2024
The snps_GARB.txt file. I sent to your email
from syri.
mnshgl0110
commented on August 13, 2024
Hi. A blank log file is quite strange. That could mean that SyRI was not running properly at all. Could you please check the installation again, and also the command that you are using.
Also, I didn't receive any email. Could you please check that you used the right email address.
from syri.
mnshgl0110
commented on August 13, 2024
There was a bug affecting SNP identification. It should be fixed now and you should be getting proper number of SNPs.
from syri.
Related Issues (20)
- ERROR - No syntenic region found for chromosome: chr15. This is potentially caused by the two assemblies having different strands for this chromosomes. Reverse complement the chromosome to ensure that the same strands are analysed. Exiting HOT 1
- Syri doesn't deal with unequal chromosome comparison HOT 2
- IndexError: list index out of range(direction) HOT 6
- chroder input format requirements HOT 2
- ImportError: libicui18n.so.56: cannot open shared object file: No such file or directory HOT 2
- Sequence length calculation error HOT 6
- translocation ascross chromosomes HOT 1
- Can't install on Ubuntu 22.04 HOT 2
- How to cite chroder? HOT 1
- error running syri: IndexError: list index out of range HOT 2
- How to identify breakpoint of large inversion HOT 3
- Aligning bacterial genomes with different number of contigs HOT 2
- longer processing time for large genome? HOT 1
- nearly identical HDRs HOT 3
- How long does it take to generate the result file? HOT 3
- conda installation HOT 2
- Removes 'low-quality alignments' - what does this mean? HOT 1
- complicated region not detected correctly HOT 2
- About InvOut and Inv breakpoints HOT 3
- Huge chromosome problem HOT 6
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 syri.