Comments (3)
bigpocho
commented on May 29, 2024
All test passed expect DMR, i havent installed all that dependencys yet
Test importing methylpy module.
- importing call_mc_se: pass
- importing call_mc_pe: pass
- importing DMRfind: pass
- importing parser: pass
Check methylpy executable:pass
methylpy is successfully installed!
Check whether dependencies are available in PATH
- find bowtie: failed
- find bowtie2: found version 2.3.5
- find minimap2: failed
- find samtools: found version 1.9
- find cutadapt: found version 1.18
- find java: found version 2019-07-16
Only bowtie2 is available. Skip tests for bowtie related code
Test DMRfind: failed
Test reidentify-DMR: failed
Test build-reference with bowtie2: pass
Test single-end-pipeline with bowtie2: pass
Test paired-end-pipeline with bowtie2: pass
Test quality filter for BAM file of single-end data: pass
Test call-methylation-state for single-end data: pass
Test call-methylation-state for paired-end data: pass
Test merge-allc: pass
Test filter-allc: pass
All tests are done!
from methylpy.
yupenghe
commented on May 29, 2024
Not sure if your problem is solved but you can try to provide the absolute path to your picard.jar.
from methylpy.
bigpocho
commented on May 29, 2024
Thank you for your response. Yeah it was solved. the problem was that the
picard.jar file was corrupted during the download it turn out that the
solution was to download it again.
…On Sat, Nov 2, 2019, 05:38 Yupeng He ***@***.***> wrote:
Not sure if your problem is solved but you can try to provide the absolute
path to your picard.jar.
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
<#42?email_source=notifications&email_token=AIBAF2WYZSJ676T7CYB6BL3QRT73BA5CNFSM4JH3ZVD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEC4TU7Y#issuecomment-549010047>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AIBAF2U2STI55LD6K4BUK7LQRT73BANCNFSM4JH3ZVDQ>
.
from methylpy.
Related Issues (20)
- DMRfind use two samples is ok but a lot of samples is wrong HOT 24
- Methylpy and Bismark for alignment
- Where is the methylation difference reflected in the DMRfind code HOT 11
- Average methylation level of a sample HOT 1
- DMRfind fails with key error 179 HOT 2
- run_test.py fails HOT 21
- cutadapt error for methylpy v 1.4.6 HOT 3
- Running RMS tests failed. HOT 18
- Ubuntu Optional step to Compile rms.cpp is formatted wrong HOT 1
- bam-quality-filter NOMe-seq HOT 2
- Methylation calling in non-directional libraries HOT 1
- Help for parameters tuning.
- mapping to a large genome HOT 1
- Methylpy in plant HOT 7
- DMR HOT 4
- binom-test failed HOT 15
- DMRfind-Histogram FDR correction did not converge. HOT 1
- NAs of methylpy add-methylation-level result HOT 5
- low align rate conflicting with bismark align rate HOT 4
- how to acquire or calculate the mapping efficiency using methylpy? 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 methylpy.