Comments (5)
Upon isolating the run_drimseq_filter.R script in ./bin/ and running it on the specific input files and arguments, it would seem R does not recognize the filtering arguments as numerics, but rather as strings:
run_drimseq_filter.R: Line 27
min_samps_gene_expr <- args[4]
min_samps_feature_expr <- args[5]
min_samps_feature_prop <- args[6]
min_feature_expr <- args[7]
min_feature_prop <- args[8]
min_gene_expr <- args[9]
Thus comparisons later on fail, perhaps force the arguments into numbers will solve the problem. Weirdly enough, when I first installed the rnasplice pipeline and ran the test profile, everything worked.
from rnasplice.
I followed the same process, with running run_drimseq_filter.R myself, and when changing the class to numeric does solve the error, and when chancing the class to a character recreates the error "min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE" in the DRIMSeq::dmFilter function.
So the fix should be stating the class to numeric of the args in line 27.
from rnasplice.
Hello @DwinGrashof
Casting to numeric definitely seems like the correct fix. Could you also provide your nextflow.log and a snippet of the process which shows the command line which is run for run_drimseq_filter.R
Thanks!
from rnasplice.
Hello @DwinGrashof and @bio-info-guy
We have just generated a v1.0.1 release with the patch discussed above. Please give it a try and let us know if it has fixed your issue.
from rnasplice.
Dear @jma1991 ,
Patch v1.0.1 seems to have solved the min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE
issue as expected.
I am running into another issue with stageR now, but I will post this first on the slack channel, and make a separate issue if necessary.
This issue can be closed, thanks a lot!
from rnasplice.
Related Issues (20)
- Missing rMATS arguments HOT 2
- DEXSeq-DTU Stager pScreenAdjusted HOT 1
- sashimi_plot error HOT 2
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The processes for splitting files are running very slowly with large numbers of input samples HOT 5
- Error: suppa_split_file.R Input_file must contain samplesheet samples. HOT 2
- ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)' HOT 11
- Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) HOT 3
- Error single-end execution HOT 1
- Error in SUPPA: Clustergroups are assigned incorrectly HOT 4
- Miso error HOT 10
- `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` HOT 7
- RNA splice output
- Merged genes output HOT 3
- DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER not working with special characters in sample names
- AWSmegatests are failing HOT 5
- Spare memory for samtools issue HOT 1
- Implement IsoformSwitchAnalyzeR HOT 2
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 rnasplice.