Comments (4)
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.
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.
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.
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
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from tsrnasearch.