# Cut Issue Related to Metagenomic **URL:** \ **Category:** usegalaxy.org support\ **Tags:** queued-gray-datasets, tool-help, cut1\ **Created:** [April 30, 2026, 2:14pm UTC](https://help.galaxyproject.org/t/cut-issue-related-to-metagenomic/17698 "2026-04-30T14:14:52Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Arif\_Omar](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/arif_omar/32/8632_2.png) [@Arif\_Omar](https://help.galaxyproject.org/u/Arif_Omar)\ **Post date:** [April 30, 2026, 2:14pm UTC](https://help.galaxyproject.org/t/cut-issue-related-to-metagenomic/17698/1 "2026-04-30T14:14:52Z")
Hi, I am trying to use the cut on my “Predicted taxon relative abundance (output of Metaphlan)” but it seems like it has taken more than 30 minutes now. Am i doing anything wrongly here? I have also tried to cut c1,c3 another is c1,c3,c5 like the ones mentioned in the tutorial ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 30, 2026, 10:03pm UTC](https://help.galaxyproject.org/t/cut-issue-related-to-metagenomic/17698/2 "2026-04-30T22:03:42Z")
Welcome @Arif_Omar We can probably help! If you job is only queued, you can wait a bit longer or you can welcome to [generate a share link to your history](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) and we can help to confirm the state, including making sure that the inputs appear to be ready to process and appropriate for the tool/parameters used. How to interpret the job state is below! Even “small” jobs can queue. Later on when using a workflow this won’t matter as much. 🙂 ### Job status The first item to check is whether the job is queued or if it is executing already. A queued job seems possible for the 30 minute time frame but an executing job would be very odd to last this long! * * * #### Compare the color of your datasets to these job processing stages. - **Grey** : The job is queued. Allow this to complete! - **Yellow** : The job is executing. Allow this to complete! - **Green** : The job has completed successfully. - **Red** : The job has failed. Check your inputs and parameters with Help examples and GTN tutorials. Scroll to the bottom of the tool form to find these. - **Light Blue** : The job is paused. This indicates either an input has a problem or that you have exceeded the disk quota set by the administrator of the Galaxy instance you are working on. - **Grey, Yellow, Grey again** : The job is waiting to run due to admin re-run or an automatic fail-over to a longer-running cluster. ⚠ Don’t lose your queue placement! **It is _essential_ to allow queued jobs to remain queued, and to never interrupt an executing job.** If you delete/re-run jobs, they are added back to the _end of the queue again_. Related FAQs - [Troubleshooting errors](https://galaxyproject.github.io/training-material/faqs/galaxy/analysis_troubleshooting.html) - [My jobs aren’t running!](https://galaxyproject.github.io/training-material/faqs/galaxy/analysis_jobs_not_running.html) * * * With another summary here with some practical help: > [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1): > > ⏰ When working at [UseGalaxy.org](http://UseGalaxy.org), [UseGalaxy.eu](http://UseGalaxy.eu), or [UseGalaxy.org.au](http://UseGalaxy.org.au), your analysis jobs execute [at large scale academic clusters](https://training.galaxyproject.org/training-material/faqs/galaxy/#analysis). Hundreds of thousands of jobs process each month! > > - Use a [Workflow](https://training.galaxyproject.org/training-material/search2?query=workflow) for batch work. > - Allow [queued (grey color) and executing (yellow-orange) datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_job_status.html) to finish processing. > - Deleting and rerunning puts your job back _at the end_ of the queue again! > - Job priority is the exactly the same for everyone. > - **Be patient**. Galaxy is a free service, when a lot of people are using it, [you may have to wait longer than usual](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_jobs_not_running.html) (especially for ‘big’ jobs, e.g. alignments). * * * * * * ### Queued job state From there, a queued job (gray in color) can be examined closer to learn more about why the job may be waiting to run! Check the input to your **Cut** jobs. 1. Is the upstream job still processing or has it completed (green dataset). 2. Tools process once there are available inputs and a place on the cluster to run it! 3. Review these inputs to make sure the data is not empty, or in an error state, or in a paused job state! Your job queues as soon as the tool is submitted, even if the inputs isn’t ready yet. This is one reason why _using a workflow to queue everything at once_ is so helpful! * * * ### Executing job state Executing jobs (yellow in color) have been sent out to a cluster node for processing. Galaxy captures some technical metrics about a job and the job environment while it is away, but the total job must complete before details are returned (outputs, detailed logs). This is a bit different from running a tool on a single computer where everything is local and intermediate results can be inspected, or job logs reported in real-time. Instead, Galaxy processes jobs across a distributed cluster network, similar to how nodes process jobs on a university cluster, or at a commercial cloud cluster. Allowing a job to completely process is how to get results and logs! * * *