Bicycle Permissions error

[SriAnushaMatta]

I am new to bicycle and have downloaded sample data from the bicycle website (Data for E.Coli)

After the project creation, we ran the following command:

java -jar /home/admin1/Downloads/bicycle-1.8.2/bicycle-1.8.2.jar reference-bisulfitation -p data/myproject/

We get errors that the location is not accessible or not available though we have created the directory previously. Is this an error anyone has faced?

SEVERE: Error during execution

java.lang.IllegalArgumentException: Cannot find /run/user/1000/gvfs/smb-share or it is not a directory, or it is not accessible at es.cnio.bioinfo.bicycle.Sample.buildSamples(Sample.java:122) at es.cnio.bioinfo.bicycle.Project.readFromDirectory(Project.java:268) at es.cnio.bioinfo.bicycle.cli.ProjectCommand.execute(ProjectCommand.java:50) at es.cnio.bioinfo.bicycle.cli.CLIApplication.run(CLIApplication.java:86) at es.cnio.bioinfo.bicycle.cli.Main.main(Main.java:27)

• We have the administrative login and no password has been asked.

  • The Java version is 11.0.7

  I am attaching a screen shot of the error.

Please help with this error.

[lipido]

Hello,

Didi you check that the directory exists? What is the output of this command?: ls -l /run/user/1000/gvfs/smb-share

[SriAnushaMatta]

Hello, This command has the following output:

No such file or directory

[lipido]

So, it is normal that bicycle gives this error. Do you recognize this directory? What command did you use to create the project with bicycle?

[SriAnushaMatta]

Hello,

This was the command that we used to create the project.

This command worked:

-jar /home/admin1/Downloads/bicycle-1.8.2/bicycle-1.8.2.jar create-project -p data/myproject -r sample-data/ref-genomes -f sample-data/reads/sample-1

The next command gave us the error mentioned in the query:

-jar /home/admin1/Downloads/bicycle-1.8.2/bicycle-1.8.2.jar reference-bisulfitation -p data/myproject

[SriAnushaMatta]

We had also tried in another system, we face the following error:

Unable to access jarfile /Bicycle/bicycle-1.8.2/bicycle-1.8.2.jar

This happens though we have administrative privileges.

[lipido]

Please, give me the output of the config.txt file inside your project.

[SriAnushaMatta]

Hello,

This is the output:

project_directory:/run/user/1000/gvfs/smb-share:server=xyz-backup.local,share=backup/backup/Anusha/data/myprojectreference_directory:/run/user/1000/gvfs/smb-share:server=xyz-backup.local,share=backup/backup/Anusha/data/ref_genomes reads_directory:/run/user/1000/gvfs/smb-share:server=xyz-backup.local,share=backup/backup/Anusha/data/reads paired:false directional:true

[lipido]

It seems that the project_directory is strange (/run/user/1000/gvfs/smb-share:server=xyz-backup.local,share=backup/backup/Anusha/data/myproject).

Give me the full path where config.txt is located (aka the project directory)

[SriAnushaMatta]

Hello,

This is the path:

myproject is the name of the project and the following is the path.

/run/user/1000/gvfs/smb-share:server=xyz-backup.local,share=backup/backup/Anusha/data/myproject