# Pre.cluster hanging on sample processing

**URL:** <https://forum.mothur.org/t/pre-cluster-hanging-on-sample-processing/19949>\
**Category:** Commands in mothur\
**Created:** [June 7, 2019, 6:50pm UTC](https://forum.mothur.org/t/pre-cluster-hanging-on-sample-processing/19949 "2019-06-07T18:50:49Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![cgivens](https://avatars.discourse-cdn.com/v4/letter/c/9d8465/32.png) [@cgivens](https://forum.mothur.org/u/cgivens)\
**Post date:** [June 7, 2019, 6:50pm UTC](https://forum.mothur.org/t/pre-cluster-hanging-on-sample-processing/19949/1 "2019-06-07T18:50:49Z")

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I am trying to process a large data set on our High Performance Computing Cluster - all steps have processed fine but when I get to the pre.cluster step, it seems to hang on and stall at processing a specific sample. I haven’t received an error and it has not updated files for over 8 days. I have tried running this process on 1.41.1 and 1.41.2. I have run this same script on other data sets and never had this issue before. I have tried it with different processors (1, 2, 8, and 48, 100) to see if that would influence the run - at the 48 and 100 processors, the process did “kill” itself.

pre.cluster(fasta=AmphStability.trim.contigs.good.unique.good.filter.unique.fasta, count=AmphStability.trim.contigs.good.unique.good.filter.count\_table, diffs=4, processors=8)

I can share my data files if there might be an issue there.

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [June 10, 2019, 5:49pm UTC](https://forum.mothur.org/t/pre-cluster-hanging-on-sample-processing/19949/2 "2019-06-10T17:49:13Z")

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Hi - can you try the latest version - [1.42.1](https://github.com/mothur/mothur/releases/tag/v1.42.1)? We made a few improvements that should speed things up and cause mothur to use less RAM.

Pat

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<div class="post-metadata">

**Author:** ![cgivens](https://avatars.discourse-cdn.com/v4/letter/c/9d8465/32.png) [@cgivens](https://forum.mothur.org/u/cgivens)\
**Post date:** [June 17, 2019, 7:09pm UTC](https://forum.mothur.org/t/pre-cluster-hanging-on-sample-processing/19949/3 "2019-06-17T19:09:02Z")

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Upgrading to 1.42.1 solved the issue - thanks!

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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [June 27, 2019, 7:09pm UTC](https://forum.mothur.org/t/pre-cluster-hanging-on-sample-processing/19949/4 "2019-06-27T19:09:04Z")

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