# Annotation of bins with Prokka

**URL:** <https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540>\
**Category:** usegalaxy.org support\
**Tags:** prokka, server-side-error\
**Created:** [February 16, 2022, 4:04pm UTC](https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540 "2022-02-16T16:04:29Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![mjordanr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mjordanr/32/3135_2.png) [@mjordanr](https://help.galaxyproject.org/u/mjordanr)\
**Post date:** [February 16, 2022, 4:04pm UTC](https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540/1 "2022-02-16T16:04:29Z")

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Hello everyone!  
I assembled raw and trimmed reads (Illumina PE150) using metaSPAdes and then clustered into bins with MaxBin2. Now I want to annotate these bins by using Prokka but I’ve got this error:

Argument “1.7.8” isn’t numeric in numeric lt (\<) at /usr/local/bin/prokka line 259.  
Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/040/759/40759167/\_job\_tmp -Xmx28g -Xms256m  
Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/040/7

I’ve uploaded the bins obtained from MaxBin2 in fasta format.

Could anyone help me with that?

 ![error](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/17c387538a0bdb0700ac7955818ab678380b0b80.jpeg)

Thank you in advance!

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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:** [February 16, 2022, 5:41pm UTC](https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540/2 "2022-02-16T17:41:53Z")

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**Update:**

The tool is now running correctly. Please try again.

Thank you to everyone who reported the problem 🙂

* * *

Hi @mjordanr

The tool has a new known configuration issue specific to [UseGalaxy.org](http://UseGalaxy.org). The fix is in progress but not completely done yet. Tracking ticket: [Prokka 1.14.6+galaxy1 = missing dependency · Issue #354 · galaxyproject/usegalaxy-playbook · GitHub](https://github.com/galaxyproject/usegalaxy-playbook/issues/354)

Meanwhile, please run the tool at a different public Galaxy server. Both of these are good choices and host a toolset similar to the US server: [UseGalaxy.eu](http://UseGalaxy.eu) or [UseGalaxy.org.au](http://UseGalaxy.org.au).

Thanks for reporting the problem!

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<div class="post-metadata">

**Author:** ![mjordanr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mjordanr/32/3135_2.png) [@mjordanr](https://help.galaxyproject.org/u/mjordanr)\
**Post date:** [February 16, 2022, 7:00pm UTC](https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540/3 "2022-02-16T19:00:24Z")

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Hello!  
Thank you for your answer. Before you replied, I tried to run Prokka on [galaxy.eu](http://galaxy.eu) and worked so I figured it was something happening with the main server.  
Again, thanks 🙂

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<div class="post-metadata">

**Author:** ![mjordanr](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/mjordanr/32/3135_2.png) [@mjordanr](https://help.galaxyproject.org/u/mjordanr)\
**Post date:** [February 16, 2022, 7:06pm UTC](https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540/4 "2022-02-16T19:06:13Z")

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Sorry to bother you again,  
I runned Bowtie2 in order to get the relative abundance of each bin by mapping reads to each bin. However, I only obtained the alignment output file and not a pdf / html to see the data results.  
I set the following parameters:

Paired-end library:  
File #1 Trimmed \_1.fq.gz R1 paired  
File #2 Trimmed \_2.fq.gz R2 paired  
Reference genome: use a genome from the history and build index  
Select reference genome: upload all bins downloaded previously from MaxBin \> select all bins \> execute

Any idea of what’s happening?  
Thank you

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<div class="post-metadata">

**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:** [February 16, 2022, 8:21pm UTC](https://help.galaxyproject.org/t/annotation-of-bins-with-prokka/7540/5 "2022-02-16T20:21:37Z")

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Hi @mjordanr – not a problem 🙂 I can explain

- `Bowtie2` will report mapping statistics in the Job Details report ( ℹ per dataset) with default settings.

- To get those stats reported into a distinct dataset output, toggle the option “Save the bowtie2 mapping statistics to the history” to YES.

- The tool `MultiQC` will generate a graphical output of statistics created by `Bowtie2`. It will also parse text output from many other tools, including tools that generate alternative statistics from `BAM` datasets.

I would suggest first examining how the `Bowtie2` stats are graphed by `MultiQC`, then if that isn’t what you need, review what other tools are available that might report what you are interested in (check the `MultiQC` pull-down tool menu), then run those selected tools on the `BAM` dataset and input those outputs to `MultiQC`. You could layer in multiple tool outputs into the same `MultiQC` report to batch stats generated by different summary tools (and on different `BAM`s) all into one single report.

That might involve a lot of clicking at first! Once you determine the statistical tool(s) of interest, consider creating/extracting a short workflow for the whole process. You can hide intermediate steps/datasets to reduce clutter in the history (meaning, only report the final graphical report) plus mark the workflow itself to display in the Tool Panel – it will be listed just like a single “tool” and can be used like one. Workflow tutorials [Search Tutorials](https://training.galaxyproject.org/training-material/search?query=workflow)

Hope that helps!