Comments (3)
No, this is not normal. Can you share the current log file? If it did not take too long to reach the 'generating table output ' step, then can you rerun syri with log level debug and then share the log file as well.
from syri.
No, this is not normal. Can you share the current log file? If it did not take too long to reach the 'generating table output ' step, then can you rerun syri with log level debug and then share the log file as well.
It's weird, it finally ran the results correctly on the night of the 12th. I guess it may be because the input file was too large, which resulted in a long running time? I ran another execution with a smaller input file before, and it only took three hours to generate the result file.
from syri.
For very complex (rearranged with multiple TEs) genomes, syri can take some time but even then Generating table output
should not take so long. Are you working with large genomes that are quite diverged (have multiple SNPs and indels)?
Nevertheless, good that it finished successfully. If possible, can you run syri on the large dataset with log-level debug and then share the syri.log file? It would help my in finding the bottleneck. NOTE: if rerunning syri, then do that in a different folder so that the current output do not get overwritten.
from syri.
Related Issues (20)
- 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
- keyerror HOT 3
- Request for Guidance on Converting NOTALs to Presence in Syri Outputs HOT 3
- translocated to different chromosomes HOT 3
- Consult DUP/INVDP for details HOT 2
- microhomology at ends of insertions HOT 4
- INV vs INVDUP HOT 2
- ERROR syri:201 - Length of query sequence of Chr1 is less than the maximum coordinate of its aligned regions HOT 7
- Wrong CIGAR string HOT 1
- IndexError: list index out of range syri HOT 9
- SYRI:IndexError: list index out of range HOT 1
- how to merge SyRI vcfs HOT 2
- Questions about 'NOTAL' HOT 2
- Question about output
- Support for promer HOT 3
- CIGAR string starting with non-matching base HOT 1
- Overlapping INV and SYN 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 syri.