# Where to report issues with QuNex

Issues are to be reported on the QuNex user forum here: [https://forum.qunex.yale.edu/](https://forum.qunex.yale.edu/). See also the [Forum Issue Reporting Guide](https://forum.qunex.yale.edu/t/qu-nex-issue-reporting-guide/27), and an example of a forum post issue report [here](https://forum.qunex.yale.edu/t/using-runpalm-on-parcellated-data-gives-error-using-permute/58).

To report an issue please generate an issue report following the convention described below.

## How to report issues with QuNex

If we (the QuNex developers) do not have access to your file system, please follow the **Description Call Logs** (DCL) issue reporting specification:

- *Description of issue* – Detailed description of issue and the workflow/analysis during which the issue was encountered.
- *Call* – The exact, explicit and full call you used. This allows us to replicate and resolve the problem you need to provide all elements of the code (the batch.txt file, call parameters …). If several commands were ran in a sequence this also provides calls to prior commands.
- *Logs and outputs* – All logs (runlogs and comlogs found in the processing/logs folder) and outputs (stdout and stderr terminal outputs and errors) associated with the execution of the command. This can be included in your report as an attachment.

If we do have access to your file system, please use the **Description Call Path** (DCP) convention to report an issue.

- *Description of issue* – Detailed description of issue and the workflow/analysis during which the issue was encountered.

- *Call* – The exact, explicit and full call you used. To allows us to replicate and resolve the problem you need to provide all elements of the code (the batch.txt file, call parameters …). If several commands were ran in a sequence this also provides calls to prior commands.

- *Path* – Exact and absolute paths for the code used in the call, the data used in the call, and any logs/outputs that may be been produced. Please ensure that we have access to these directories on your file system, so we are able to replicate and resolve the error.

## An example of reporting issues with QuNex

### If we have DO NOT have access to your file system

**Title:**

setup_hcp issue with `folderstructure` argument

**Description:**

I’m getting an invalid arguments error when running setup_hcp step.
This step works correctly if I am using the default folderstructure (hcpls), however when trying to use the `folderstructure=initial` argument then the command fails.

**Call:**

The command I ran, with the container tag `qunex_suite-0_48_19_test.sif`, is:

``` bash
sshcpu
for file in CC720358; do \
 qunex_container setup_hcp \
     --sfolder="/gpfs/project/fas/n3/Studies/ThalDev/sessions/$file" \
     --folderstructure='initial' \
     --container="/gpfs/project/fas/n3/software/Apptainer/qunex_suite-latest.sif"; \
done
```

**Logs:**

StdOut:

``` bash
Quantitative Neuroimaging Environment & Toolbox (QuNex) Suite Version 0.48.19

ERROR: Extra argument folderstructure is not valid! Please check your command!
ERROR in running setup_hcp:

Invalid arguments

The extra argument(s) provided is/are not valid! [folderstructure]

The call received was:
(please note that when run through scheduler, all possible parameters,
even non relevant ones are passed)

qunex setup_hcp \
    --sfolder=/gpfs/project/fas/n3/Studies/ThalDev/sessions/CC720358 \
    --folderstructure=initial

Please run `qunex ?setup_hcp` to get help for the failed command.
The command does not generate output files.
```

StdErr:

``` bash
ERROR: Extra argument folderstructure is not valid! Please check your command!
ERROR in running setup_hcp:

Invalid arguments

The extra argument(s) provided is/are not valid! [folderstructure]
```

### If we have DO have access to your file system

**Title:**

setup_hcp issue with `folderstructure` argument

**Description:**

I’m getting an invalid arguments error when running setup_hcp step.
This steps works correctly if I am using the default folderstructure (hcpls), however when trying to use the `folderstructure=initial` argument then the command fails.

**Call:**

The command I ran, with the container tag `qunex_suite-0_48_19_test.sif`, is:

``` bash
sshcpu
for file in CC720358; do \
qunex_container setup_hcp \
 --sfolder="/gpfs/project/fas/n3/Studies/ThalDev/sessions/$file" \
 --folderstructure='initial' \
 --container="/gpfs/project/fas/n3/software/Apptainer/qunex_suite-latest.sif"; \
done
```

**Path:**
I ran this analysis on Yale HPC's Grace cluster.

The script I used to run qunex is located here on Grace: `/gpfs/project/fas/n3/Studies/ThalDev/processing/scripts/CamCan_processing.sh`

The data are located here: `/gpfs/project/fas/n3/Studies/ThalDev/sessions/CC720358/`

The logs are located here: `/gpfs/project/fas/n3/Studies/ThalDev/processing/logs/comlogs` and `/gpfs/project/fas/n3/Studies/ThalDev/processing/logs/runlogs`