Annotation of bins with Prokka

usegalaxy.org support
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1

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
error661×653 87.2 KB

Thank you in advance!

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2

Update:

The tool is now running correctly. Please try again.

Thank you to everyone who reported the problem :slight_smile:

Hi @mjordanr

The tool has a new known configuration issue specific to 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

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 or UseGalaxy.org.au.

Thanks for reporting the problem!

3

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

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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

5

Hi @mjordanr – not a problem :slight_smile: I can explain

  • Bowtie2 will report mapping statistics in the Job Details report ( :information_source: 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 BAMs) 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

Hope that helps!