task 1 failed - "The active subnetwork file does not exist! Check the `active_snw_path` argument"

[ajawd]

hello, i am facing problems with this package even if i use your saved data example am using R studio Version 1.2.5001 and pathfindR version ‘1.4.0’ the error say task 1 failed - "The active sub network file does not exist! Check the active_snw_path argument"

[egeulgen]

can you share the commands you ran to reproduce the issue? Is this "RA_input" or "myeloma_input"?

You should have java installed on your system as well. I strongly suspect that's the reason for this issue

For future reference, please use the bug report template so that this works faster

[ajawd]

i used RA input library(pathfindR) knitr::kable(head(RA_input)) RA_output <- run_pathfindR(RA_input)

this is the command i run

n_processes is set to iterations because iterations < n_processes There is already a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(5)" not to overwrite any previous results.

Testing input

The input looks OK

Processing input. Converting gene symbols,

      if necessary (and if human gene symbols provided)

Number of genes provided in input: 572 Number of genes in input after p-value filtering: 572

Could not find any interactions for 11 (1.92%) genes in the PIN Final number of genes in input: 561

Performing Active Subnetwork Search and Enrichment

Error in { : task 1 failed - "The active subnetwork file does not exist! Check the active_snw_path argument" i have also installed java in my computer

[ajawd]

windows version 10 java version 8 (build 1.8.0_231-b11) R studio Version 1.2.5001 pathfindR version ‘1.4.0’

[egeulgen]

RA_input was tested with run_pathfindR on multiple platforms so this is very odd. Can you try a manual run? see here

[ajawd]

i have run the manual code as you told me there is also error massage in this command active_snws <- active_snw_search(processed_data, pin_path, snws_file = "subnetworks", search_method = "GR")

Error in pathfindR::filterActiveSnws(active_snw_path = snws_file, sig_genes_vec = input_for_search$GENE, :

The active subnetwork file does not exist! Check the active_snw_path argument

[ajawd]

dear sir, i have run the manual code as you told me there is also error massage in this command active_snws <- active_snw_search(processed_data, pin_path, snws_file = "subnetworks", search_method = "GR")

Error in pathfindR::filterActiveSnws(active_snw_path = snws_file, sig_genes_vec = input_for_search$GENE, :

The active subnetwork file does not exist! Check the active_snw_path argument On Monday, November 11, 2019, 9:49:43 AM GMT+8, Ege Ulgen notifications@github.com wrote:

RA_input was tested with run_pathfindR on multiple platforms so this is very odd. Can you try a manual run? see here

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[ajawd]

i hope sir you replay to me soon i need to finish my work and use your package if possible. appreciated zeinab On Monday, November 11, 2019, 12:59:49 PM GMT+8, Zeinab Mohamed zeinabmohamed86@yahoo.com wrote:

dear sir, i have run the manual code as you told me there is also error massage in this command active_snws <- active_snw_search(processed_data, pin_path, snws_file = "subnetworks", search_method = "GR")

Error in pathfindR::filterActiveSnws(active_snw_path = snws_file, sig_genes_vec = input_for_search$GENE, :

The active subnetwork file does not exist! Check the active_snw_path argument On Monday, November 11, 2019, 9:49:43 AM GMT+8, Ege Ulgen notifications@github.com wrote:

RA_input was tested with run_pathfindR on multiple platforms so this is very odd. Can you try a manual run? see here

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[egeulgen]

Is there a directory called "active_snw_search" containing "input_for_search.txt' as well "subnetworks.txt"?

It's possible that you do not have write permissions in the working directory you're running the analysis. try running file.access(".", 2) and the output is 0 for success and -1 for failure.

[ajawd]

i have inside my directory file generated called "active_snw_search" containing "input_for_search.txt' but no such file called "subnetworks.txt" file.access(".", 2) i have run this code and the result was 0 which is sucess today i have tried to run this code again it work so how i suppose to see the results ? because after i run both codes library(pathfindR) processed_data <- input_processing(input = RA_input, p_val_threshold = 0.05, pin_name_path = "Biogrid", convert2alias = TRUE) pin_path <- return_pin_path(pin_name_path = "Biogrid") active_snws <- active_snw_search(processed_data, pin_path, snws_file = "subnetworks", search_method = "GR") enrichment_res <- enrichment_analyses(snws = active_snws, sig_genes_vec = input_processed$GENE, pin_name_path = "Biogrid", genes_by_term = kegg_genes, term_descriptions = kegg_descriptions) what should i do next? i would like to present the results as you showed in biostars

[ajawd]

i have tried also to run the code RA_output <- run_pathfindR(my data) the results always the same

n_processes is set to iterations because iterations < n_processes There is already a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(5)" not to overwrite any previous results. ## Testing input The input looks OK ## Processing input. Converting gene symbols, if necessary (and if human gene symbols provided) Number of genes provided in input: 572 Number of genes in input after p-value filtering: 572 Could not find any interactions for 11 (1.92%) genes in the PIN Final number of genes in input: 561 ## Performing Active Subnetwork Search and Enrichment ## Processing the enrichment results over all iterations ## Annotating involved genes and visualizing enriched terms Downloading pathway diagrams of 93 KEGG pathways | | 0%Cannot reach URL, please check your connection: hsa03040 Here's the original error message: 'wget' call had nonzero exit statusError in tryCatch({ : object 'status' not found

 

[egeulgen]

ok, the latest error you get is related to a connection issue: 'wget' call had nonzero exit statusError. You could (a) figure out what is the issue with wget or (b) run pathfindR without visualizing colored pathway diagrams, i.e. output_df <- run_pathfindR(input_df, visualize_enriched_terms = FALSE).

I will make some changes so that when downloading a KEGG file fails, the visualization for that pathway is skipped and close this issue as the error you get is no longer related to pathfindR but wget.

[ajawd]

Dear Sir, I have send you messages at github but it seems that you are busy so didn't replay. The issues appear in the package can't be solved by me or any one expertise beside you that is why realing of the package compromise with a lot of questions and issues.  I really like your package I would like to use it all with visualization.  Could you politely read my messages  at github the last two messages?  appreciated your time and efforts  Zeinab PhD student , department of bioinformatics and genomics China pharmaceutical university 

Sent from Yahoo Mail on Android

On Mon, Nov 11, 2019 at 5:13 PM, Ege Ulgennotifications@github.com wrote:
Is there a directory called "active_snw_search" containing "input_for_search.txt' as well "subnetworks.txt"?

It's possible that you do not have write permissions in the working directory you're running the analysis. try running file.access(".", 2) and the output is 0 for success and -1 for failure.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[egeulgen]

Dear @ajawd, I did read all your messages and explained that the error seems to be related to wget as you get the error 'wget' call had nonzero exit status.

I also made changes the package so that when downloading a KEGG file fails, the visualization for that pathway is skipped. To be able to run pathfindR with this changes, please install the development version via:

install.packages("devtools") # if you have not installed "devtools"
devtools::install_github("egeulgen/pathfindR")

Do let me know if you have any further questions, Best, -E

[nahid18]

@ajawd, I have faced the similar issue. I installed Java and the issue went away.

IMPORTANT NOTE For the active subnetwork search component to work, the user must have Java (>= 8.0) installed, and the path/to/java must be in the PATH environment variable.

Install Java in your operating system.