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BioinformaticsLabAtMUN / sRNARFTarget

A random forest-based model to predict transcriptome-wide targets of sRNAs.
GNU General Public License v3.0
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Failed to Create All possible pairs #2

Closed LukeActon closed 2 years ago

LukeActon commented 2 years ago

Hi there,

Im trying to use sRNARFTarget using a virtual machine. At the moment im just using the Ecoli dataset providedin the github repository. When I run the .nf script, it always fails creating all possible pairs.

Error executing process > 'createAllPossiblePairs'

Caused by: Process createAllPossiblePairs terminated with an error exit status (1)

Im running the programme with the Docker container provided, any idea whats causing this?

Thanks!

LukeActon commented 2 years ago

.command.log

Seems like im unable to create symbolic links, do you know of a work around for this?

BioinformaticsLabAtMUN commented 2 years ago

Hello,

What operating system are you using? and do you have permissions to write on the directory nextflow is creating the work directory?

Best,

On Tue, Jan 18, 2022 at 11:51 AM LukeActon @.***> wrote:

.command.log https://github.com/BioinformaticsLabAtMUN/sRNARFTarget/files/7890154/default.command.log

Seems like im unable to create symbolic links, do you know of a work around for this?

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LukeActon commented 2 years ago

Hi there Many thanks for getting back to me!

Im using a linux virtual machine, connected to a HPC

I do have permission to write on the directory im using.

BioinformaticsLabAtMUN commented 2 years ago

I think the issue may be with the virtual machine and not with sRNARFTarget.

Based on these posts: https://kb.vmware.com/s/article/1007277 and https://www.speich.net/articles/en/2018/12/24/virtualbox-6-how-to-enable-symlinks-in-a-linux-guest-os/ It seems virtual machines may not allow symbolic links.

Try checking whether symbolic links are enabled on your virtual machine.