# Job fail in one element of the list stops the whole pipelin

**URL:** <https://help.galaxyproject.org/t/job-fail-in-one-element-of-the-list-stops-the-whole-pipelin/8358>\
**Category:** usegalaxy.org support\
**Tags:** variant-analysis\
**Created:** [July 25, 2022, 11:08am UTC](https://help.galaxyproject.org/t/job-fail-in-one-element-of-the-list-stops-the-whole-pipelin/8358 "2022-07-25T11:08:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Alan](https://avatars.discourse-cdn.com/v4/letter/a/a87d85/32.png) [@Alan](https://help.galaxyproject.org/u/Alan)\
**Post date:** [July 25, 2022, 11:08am UTC](https://help.galaxyproject.org/t/job-fail-in-one-element-of-the-list-stops-the-whole-pipelin/8358/1 "2022-07-25T11:08:53Z")

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Dear everyone!

I am currently analysing the output of a PE sequencing of 96 samples. I have uploaded the reads and included them into a list to use the tools more efficiently. I am running a workflow using snippy, snippy core, Clustal and so. My problem is that 4/96 snippy jobs failed due to memory allocation problems and that interrupted the whole workflow. Even if I delete the failed runs, the output list is marked in red and cant resume the workflow.  
My question is: Is there a way for me to run the failed snippy jobs and include the output in the list of the successful ones in order to continue with my workflow?  
I have thought of downloading the successful runs output, running the failed ones again, download these outputs and then after re uploading everything again make a new list but my problem is that the snippy output and the bam files are 54Gb each, way too heavy for me to do.  
I really appreciate your assistance on this 🙂

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**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:** [September 22, 2022, 12:22am UTC](https://help.galaxyproject.org/t/job-fail-in-one-element-of-the-list-stops-the-whole-pipelin/8358/2 "2022-09-22T00:22:01Z")

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Hi @Alan

> [@Alan](#):
>
> My question is: Is there a way for me to run the failed snippy jobs and include the output in the list of the successful ones in order to continue with my workflow?

There are two primary solutions for this situation:

1. Instead of deleting failed jobs, rerun instead. The bottom of the tool form will have an extra option to resume dependencies in a way that replaces the original failed datasets.

2. Remove failures during the original workflow run. [tools-that-manipulate-elements-within-a-collection](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/collections/tutorial.html#tools-that-manipulate-elements-within-a-collection)

More workflow and collection help is here, including examples of programmatically controlled workflow execution.

> **[Galaxy Training: Using Galaxy and Managing your Data](https://training.galaxyproject.org/training-material/topics/galaxy-interface/)**
>
> A collection of microtutorials explaining various features of the Galaxy user interface and manipulating data within ...