Comments (5)
@tchrisboles If I understand you correctly, yes.
You can setup another guppy_basecall_server
on another port (we generally choose 5556) on the same computer and point ru at it. For example, in the TOML the caller_settings
table will look like:
[caller_settings]
config_name = "dna_r9.4.1_450bps_fast"
host = "127.0.0.1"
port = 5556
To set up the server I would start a tmux
or screen
session and run something like so:
$ /path/to/guppy_basecall_server --config dna_r9.4.1_450bps_fast.cfg \
--port 5556 --log_path . --ipc_threads 1 --max_queued_reads 2000 \
--chunks_per_runner 48 --num_callers 1 -x cuda:all --gpu_runners_per_device 2
from readfish.
Great - will try it today and tomorrow and report. Thanks
from readfish.
Alex and Matt, I have made some progress on setting up my machine. Minknow seems to run your simulation fast5 bulk file. The unblock all test seems to work as your readme shows. However the enrich chr21,22 doesn't seem to work. The ru_summarise_fq report doesn't show the expected enhancement of mean read lengths for both chromosomes. Chr21 is slighly enhanced (but not as much as your example), and chr22 is not enhanced at all.
After 22 min of ru running using the simulation the size distributions look like:
The toml file was modified setting max_chunks to 12
I set up the guppy basecall server in a dedicated terminal window before starting Minknow like this:
Then started Minknow simulation run using your bulk fast5 file. Once the simulation started I opened a new terminal window and started ru_generators:
After 15 minutes, the mapping speeds were fairly constant, ranging between 0.08 and 0.15s.
My gpu is an RTX2080ti with 11Gb memory.
The workstation is an HP-Z8-G4 with dual Xeon processors (each 10 core), 128Gb ram, 1Tb ssd.
from readfish.
Changing to guppy server 3.4.5 seems to solve this issue - see my post in question #44.
from readfish.
Alex - in view of progress on question #44 - I think this one is closed.
from readfish.
Related Issues (20)
- Readfish and boss-runs in 2024 HOT 3
- readfish with just depletion? HOT 4
- Not being able to finish the tutorial/test HOT 6
- Provide additional TOML files which provide examples of host depletion and other use cases for readfish.
- location of readfish output HOT 4
- toml_live handling issue
- Depletion setting and unexpected behavior HOT 2
- Question about Readfish basecalling performance for messy samples HOT 6
- Playback issue HOT 14
- Problem communicating with basecaller after MinKnow update HOT 10
- Detect MinKNOW version and warn. HOT 1
- Circular Binary Segmentation HOT 3
- Having only one region in toml caused issue HOT 13
- chore: update github workflow actions HOT 1
- Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED HOT 4
- comparison between MinKNOW and Readfish HOT 4
- Error with flongle flow cell splitting HOT 5
- chore: update FAQ
- next release candidate checklist
- High count of no-barcode that map to my targets HOT 15
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 readfish.