# Nf-core/pangenome aws-megatests fail - maybe because of fusion or wave?

**URL:** <https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527>\
**Category:** Ask for help\
**Tags:** fusion, aws, nf-core\
**Created:** [February 29, 2024, 9:08am UTC](https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527 "2024-02-29T09:08:01Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![subwaystation](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/subwaystation/32/474_2.png) [@subwaystation](https://community.seqera.io/u/subwaystation)\
**Post date:** [February 29, 2024, 9:08am UTC](https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527/1 "2024-02-29T09:08:01Z")

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Hi SEQERA community,

surprisingly the aws-megatests for the nf-core/pangenome pipeline fail: [Seqera Cloud](https://tower.nf/orgs/nf-core/workspaces/AWSmegatests/watch/4MunGCoyk0WQwG). This was already extensively discussed at [Slack](https://nfcore.slack.com/archives/CTY8L26C8/p1709132002169919) but it is unclear, why. Especially, because I can’t reproduce the error on my laptop or on our SLURM cluster.

Unique to these megatests are that they use Tower, docker (wave?), and the fusion system, if I understand correctly. The pipeline always fails at the moment it wants to sort a memory mapped data structure on disk.

Thanks for any help!

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**Author:** ![jordeu](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/jordeu/32/90_2.png) [@jordeu](https://community.seqera.io/u/jordeu)\
**Post date:** [March 1, 2024, 5:55am UTC](https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527/2 "2024-03-01T05:55:35Z")

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I’ll try to reproduce it on my side. Is setting the profile “test\_full” and defining an “outdir” enough, or do I need some other configuration settings?

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**Author:** ![subwaystation](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/subwaystation/32/474_2.png) [@subwaystation](https://community.seqera.io/u/subwaystation)\
**Post date:** [March 1, 2024, 7:22am UTC](https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527/3 "2024-03-01T07:22:12Z")

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Hi @jordeu,

this would be awesome. You would also need to set two more parameters:

```auto
--n_haplotypes 8 --communities

```

The full profile is at [pangenome/conf/test\_full.config at 9740ffc4d0a00d6dc89e1c8f9579e628598d43a5 · nf-core/pangenome · GitHub](https://github.com/nf-core/pangenome/blob/9740ffc4d0a00d6dc89e1c8f9579e628598d43a5/conf/test_full.config).

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**Author:** ![jordeu](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/jordeu/32/90_2.png) [@jordeu](https://community.seqera.io/u/jordeu)\
**Post date:** [March 1, 2024, 8:39am UTC](https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527/4 "2024-03-01T08:39:50Z")

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I’ve been able to reproduce it. It is a Fusion bug. I’ve opened an internal ticket, and we are working on it.

Meanwhile, a non-ideal workaround is to set `scratch = true` only for that process.

```groovy
process {
  withName:SMOOTHXG {
      scratch = true
  }
}

```

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<div class="post-metadata">

**Author:** ![subwaystation](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/subwaystation/32/474_2.png) [@subwaystation](https://community.seqera.io/u/subwaystation)\
**Post date:** [March 1, 2024, 9:01am UTC](https://community.seqera.io/t/nf-core-pangenome-aws-megatests-fail-maybe-because-of-fusion-or-wave/527/5 "2024-03-01T09:01:49Z")

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got it, I will forward this to the nf-core community  
please ping me here, once this is fixed  
thanks!