Comments (4)
GiantSpaceRobot
commented on June 25, 2024
1
Hi there,
Nextflow cannot find a local pipeline called 'tsRNAsearch', so it is searching the nextflow-io repos for one.
Go to the directory that you downloaded tsRNAsearch (example shown below), then run the test again:
cd /home/my_name/my_tools/
nextflow run tsRNAsearch --species mouse --input_dir tsRNAsearch/ExampleData --output_dir Results --layout tsRNAsearch/additional-files/Example_Layout.csv
You don't want to be inside the tsRNAsearch directory for this!
Best,
Paul
from tsrnasearch.
alirizaaribas-ibg
commented on June 25, 2024
1
You are right. Thank you. It worked.
nextflow run tsRNAsearch --species mouse --input_dir tsRNAsearch/ExampleData --output_dir Results --layout tsRNAsearch/additional-files/Example_Layout.csv
N E X T F L O W ~ version 21.04.3
Launching `tsRNAsearch/main.nf` [focused_tuckerman] - revision: da276fb9d3
executor > local (120)
[57/d0192a] process > PREPARE_TRNA_GTF [100%] 1 of 1 ✔
[5e/755a42] process > PREPARE_NCRNA_GTF [100%] 1 of 1 ✔
[93/935238] process > TRIM_READS (1) [100%] 6 of 6 ✔
[bf/98567d] process > MAKE_STAR_DB [100%] 1 of 1 ✔
[a6/cc780b] process > STAR_ALIGN (6) [100%] 6 of 6 ✔
[b8/dfd406] process > BAM_COLLAPSE (6) [100%] 6 of 6 ✔
[14/71c244] process > ADD_EMPTY_COUNTS (TotalRNA1_trimmed_tRNAs-almost-mapped) [100%] 6 of 6 ✔
[45/63a580] process > BAM_SPLIT (6) [100%] 6 of 6 ✔
[4e/b06cd0] process > FEATURE_COUNT_TRNA (TotalRNA1_trimmed_accepted_hits_tRNAs) [100%] 6 of 6 ✔
[4b/596616] process > FEATURE_COUNT_NCRNA (TotalRNA1_trimmed_accepted_hits_ncRNAs) [100%] 6 of 6 ✔
[94/82947a] process > SUM_COUNTS [100%] 1 of 1 ✔
[3e/5989cd] process > GENERATE_TRNA_DEPTH_FILES (TotalRNA1_trimmed_accepted_hits_tRNAs) [100%] 6 of 6 ✔
[22/bc6331] process > GENERATE_MULTIMAPPER_TRNA_DEPTH_FILES (TotalRNA1_trimmed_tRNAs-almost-mapped) [100%] 6 of 6 ✔
[4b/941ce3] process > GENERATE_NCRNA_DEPTH_FILES (CytC_IP3_trimmed_accepted_hits_ncRNAs) [100%] 6 of 6 ✔
[9a/5d8d81] process > GENERATE_DEPTHFILE_STATS (CytC_IP3_trimmed_accepted_hits_ncRNAs_sorted) [100%] 12 of 12 ✔
[ba/1f2432] process > RAW_COUNTS_TO_PROPORTIONS (CytC_IP1_trimmed_accepted_hits_tRNAs) [100%] 6 of 6 ✔
[c9/ceb288] process > RAW_COUNTS_TO_NORM_COUNTS (TotalRNA2_trimmed_all-counts) [100%] 6 of 6 ✔
[7f/e5c481] process > COUNTS_TO_COLLAPSED_COUNTS (TotalRNA2_trimmed_all-counts_tpm) [100%] 12 of 12 ✔
[b9/1651c7] process > PREDICT_TSRNA_TYPE [100%] 1 of 1 ✔
[a0/dade27] process > PLOT_TRNA_ALIGNMENT_LENGTH (TotalRNA1_trimmed_accepted_hits_tRNAs) [100%] 6 of 6 ✔
[7e/063aa3] process > PLOT_TRNA_ALL_PLOTS (TotalRNA1_trimmed_accepted_hits_tRNAs_sorted) [100%] 6 of 6 ✔
[bc/b44167] process > GENERATE_RESULTS_PDF [100%] 1 of 1 ✔
[2f/50f2e3] process > DESEQ2 [100%] 1 of 1 ✔
[a0/2e6e85] process > DATA_TRANSFORMATIONS [ 0%] 0 of 1
[- ] process > DISTRIBUTION_SCORE -
[- ] process > SLOPE_SCORE -
[- ] process > CLEAVAGE_SCORE -
[- ] process > FISHERS_METHOD -
[- ] process > RESULTS_TABLE -
[- ] process > COMBINED_SCORE -
[51/bf5e5d] process > PLOT_TSRNA_LENGTHS [100%] 1 of 1 ✔
[- ] process > PLOT_TRNAS -
[- ] process > PLOT_NCRNAS -
[- ] process > VENN_DIAGRAM -
[ec/55e407] process > GENERATE_COUNT_DATAFRAME [100%] 1 of 1 ✔
[75/5fc44c] process > STACKED_BARPLOTS [100%] 1 of 1 ✔
[45/c87689] process > BARPLOTS [100%] 1 of 1 ✔
[- ] process > PREDICT_TSRNA_TYPE_GROUPS -
[- ] process > GENERATE_RESULTS_PDF_GROUPS -
[- ] process > ORGANISE_RESULTS_GROUPS -
[- ] process > PUBLISH_FILES -
from tsrnasearch.
GiantSpaceRobot
commented on June 25, 2024
Hi there,
It looks like you are running an old version of nextflow that does not support DSL2, so the tsRNAsearch pipeline won't work right now anyway. You should update the nextflow version you are using and try running the example code:
nextflow run tsRNAsearch --species mouse --input_dir tsRNAsearch/ExampleData --output_dir Results
Best,
Paul
from tsrnasearch.
alirizaaribas-ibg
commented on June 25, 2024
Hi,
I updated nextflow with nextflow self-update, another error happened:
nextflow info
Version: 21.04.3 build 5560
Created: 21-07-2021 15:09 UTC (18:09 EEST)
System: Linux 3.10.0-1062.4.1.el7.x86_64
Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 10.0.2+13
Encoding: UTF-8 (UTF-8)
Here is the output:
nextflow run tsRNAsearch --species mouse --input_dir tsRNAsearch/ExampleData --output_dir Results --layout tsRNAsearch/additional-files/Example_Layout.csv
N E X T F L O W ~ version 21.04.3
Pulling nextflow-io/tsRNAsearch ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/nextflow-io/tsRNAsearch/contents/nextflow.config
Remote resource not found: https://api.github.com/repos/nextflow-io/tsRNAsearch/contents/main.nf
from tsrnasearch.
Related Issues (13)
- Error executing process > 'BARPLOTS' during group comparision analysis HOT 1
- Whether tsRNAsearch is suitable for paired-end RNA-seq data？ HOT 2
- Error executing process > 'BARPLOTS' HOT 5
- Combined score is 0 for all features during group comparison HOT 1
- error while installing packages
- Pipeline only accepts compressed input files named .fq.gz
- Trouble installing R packages via InstallPackages.R
- CAPSULE EXCEPTION: java.io.IOException: Cannot run program "/usr/bin/java/bin/java": error=20, Not a directory (for stack trace, run with -Dcapsule.log=verbose) HOT 1
- Cannot invoke method startsWith() on null object HOT 2
- Error executing process > 'PLOT_TRNA_ALIGNMENT_LENGTH (trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs) HOT 9
- Sorting Issue HOT 1
- Pipeline throws an error when SAMcollapse.py does not return a tRNA group in group comparison analysis HOT 7
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 tsrnasearch.