Error running step3

[Avinash-git-py]

Hi,

I have installed CNest in my local system using docker and I tried to run the example commands one by one which are given in the Github. Also I tried to run the cnest.py script but I am facing an error with the usage command and facing the same error during the step 3 example command. Actually I'm not much aware of the usage and output. So could you kindly explain to me the step by step usage process along with the output interpretation.

I have attached the screenshot of the error.

The command that I have used: docker run -v "/media/ngslinux/External Disk/CNest_aug23/CNest-master/output:/output" -w "/output" -it --rm \ tomas81/cnest:dev step3 \ --indextab /media/ngslinux/External Disk/CNest_aug23/CNest-master/CNEST_NEW/index_tab.txt \ --bindir /media/ngslinux/External Disk/CNest_aug23/CNest-master/CNEST_NEW/bin \ --qc /media/ngslinux/External Disk/CNest_aug23/CNest-master/CNEST_NEW/gender_qc.txt \ --gender /media/ngslinux/External Disk/CNest_aug23/CNest-master/CNEST_NEW/gender_classification.txt \ --cov /media/ngslinux/External Disk/CNest_aug23/CNest-master/CNEST_NEW/mean_coverage.txt

The error that I have faced: usage: cnest.py [-h] [--debug] {step1,step2,step3,step4,step5} ... cnest.py: error: unrecognized arguments: Disk/CNest_aug23/CNest-master/CNEST_NEW/index_tab.txt Disk/CNest_aug23/CNest-master/CNEST_NEW/bin Disk/CNest_aug23/CNest-master/CNEST_NEW/gender_qc.txt Disk/CNest_aug23/CNest-master/CNEST_NEW/gender_classification.txt Disk/CNest_aug23/CNest-master/CNEST_NEW/mean_coverage.txt

[Avinash-git-py]

@tf2 @bshifaw @smshuai @sk-sahu

Hi,

I have sorted out the error that I have posted before. But now I'm facing errors regarding the directories and files.I have mentioned the the command and the errors below.

The command that I have used: index_tab=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt bin_dir=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/bin qc_file=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_qc.txt ender_file=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_classification.txt cov_file=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/mean_coverage.txt docker run -v "/media/ngslinux/External Disk/CNest_aug23/CNest-master/output:/output" -w "/output" -it --rm \ tomas81/cnest:dev step3 \ --indextab "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt" \ --bindir "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/bin" \ --qc "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_qc.txt" \ --gender "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_classification.txt" \ --cov "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/mean_coverage.txt"

The error that I'm facing: 08/08/2023 05:48:32 | INFO: Starting step3 08/08/2023 05:48:33 | ERROR: #Rscript /resources/run.R classify_gender /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/bin /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_qc.txt /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_classification.txt# failed with exit code 1. Loading required package: ViteRbi Loading required package: mixtools mixtools package, version 1.2.0, Released 2020-02-05 This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

Error in file(file, "rt") : cannot open the connection Calls: classify_gender -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt': No such file or directory Execution halted

I have kept the index_tab.txt in the correct path only but I don't know about this error. I have only index.bed, index.txt, index_tab.txt files from the step2 output. Is that correct output from the step2?

[tf2]

I'm sorry you have been facing these issues and sorry for not getting back to you sooner - i've been on holiday.

I am going to look into this later today and get back to you.

Curious you have a "no such file" error - as path reported looks correct given the command you are using - sorry to ask but are you absolutely sure that the file does indeed exist? And are you still having the same error?

If needed we could schedule a video call to look at this together sometime next week - if useful just let me know

[Avinash-git-py]

Hi,

Thank you for your reply.

The path for the "index_tab.txt" was correct only and I have also tried to run the same step in different directory also but still I'm facing the issue.

I have attached the index.bed, index.txt, index_tab.txt files for your reference.

[Avinash-git-py]

@tf2 index.txt index_tab.txt