Manta turn off depth option does not seem to work properly

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1

I tried to run Manta with the selection: “Set options for WES input: turn off depth filters” and it seems to be not working. Upon checking the command line generated, I could not find the “–exome” in configManta.py.
Additionally, I also check my diploidSV.vcf.gz header and it operate with the command: “##cmdline=/usr/local/bin/configManta.py --referenceFasta=localref.fa --config=./configManta.py.ini --bam=normal.bam --runDir=./MantaWorkflow --scanSizeMb=12 --callMemMb=8000”, no mention of “–exome”.
I also tried to switch to another Manta version available and replicate my job but it also did not work, too.
Have anyone encountered the same problem? What can I do?

2

Hi @hmhuongm23bio

Let’s see if I can help.

This is an example command line from the tool and I’ll break it down:

  1. reference data staging

    set -o | grep -q pipefail && set -o pipefail;
    ln -s ‘/data/dnb10/galaxy_db/files/c/7/3/dataset_c739d453-4f91-472c-9d5d-eff9678d3c38.dat’ ‘localref.fa’ && samtools faidx ‘localref.fa’ 2>&1 ||
    echo “Error running samtools faidx for Manta” >&2 &&

    This is staging the input data in the job runtime container (with error trapping).

  2. config file staging

    configManta=$(which configManta.py) && PATH=${configManta/“configManta.py”/}:$PATH && printenv && cp /opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/artbio/manta/555971edd46e/manta/configManta.py.ini configManta.py.ini &&

    Here the configuration options are first being discovered – file or form?

    Manta can take a config.ini file from the history, or the user can use the tool form options to set the workflow parameters (such as exome and the other two).

    So this step is checking which to use, then staging it into the job runtime container with the data inputs.

  3. dataset input(s) staging

    ln -s ‘/data/dnb10/galaxy_db/files/b/8/c/dataset_b8c594a1-a25c-4829-8b16-a633842d2328.dat’ normal.bam &&
    ln -s ‘/data/dnb10/galaxy_db/files/_metadata_files/d/b/a/metadata_dba3ec4b-9e09-4419-8aae-5be27cdaf7a8.dat’ normal.bai &&
    ln -s ‘/data/dnb10/galaxy_db/files/9/a/a/dataset_9aa33e0f-8892-4048-b485-4d84dfa2b19a.dat’ tumor.bam &&
    ln -s ‘/data/dnb10/galaxy_db/files/_metadata_files/d/7/0/metadata_d70e2ee2-a1d1-47d1-abab-5389b11aa738.dat’ tumor.bai &&

    Since these are BAMs, each also has an associated index.

  4. Finally, running the tool uses all three input sources above.

    configManta.py --referenceFasta=‘localref.fa’ --config=‘./configManta.py.ini’ --bam=‘normal.bam’ --tumorBam=‘tumor.bam’ --runDir=‘./MantaWorkflow’ --scanSizeMb=12 --callMemMb=8000 && python2 ‘./MantaWorkflow/runWorkflow.py’ -m local -j ${GALAXY_SLOTS:-4}

    The --config='./configManta.py.ini' value here is where the exome toggle status is input to the tool (along with the other user parameters). The rest of the content here is reconstructing how the command would be formatted on the command line plus some limits around how the job should processes (memory, threading) so the job won’t exceed what that particular cluster node can process (trapping runaway jobs from problematic inputs).

This tool works a bit differently than most of the others, mostly due to how the underlying command line tool works. Parameters are never given on the command line itself, always in a configuration file. The Galaxy wrapper always sits “around” the original tool, it doesn’t change how it was written.

Does this help? :slight_smile:

If your concern is about data content itself, try setting up a test. Choose a file that you would expect to have lines of output that would produce a different result with a different parameter settings. The GTN is usually a good resources for smaller sized test data – look in the variant calling tutorials for a source to try. Or, you can look in this tool’s directly under test-data and modify those files to trigger your test conditions.

XRef: gear → See in the ToolShed → Development repository → tools-artbio/tools/manta at main · ARTbio/tools-artbio · GitHub

3

Thank you for your reply. I did checked the config.py.ini generated (I use the “Customize a Configuration File using this Galaxy Form” option), and it seems to be used for setting up other arguments, but not for exome mode, which I believe it should be toggled from the “Additional parameters” separately.
I am confident that somehow selecting the exome mode did not work properly, as my .vcf file generated did not have --exome recorded in the command line, and also the FILTER field have some calls with “MaxDepth” flag, which should not have appeared.

4

Hi @hmhuongm23bio

I ran a test and ended up with a similar result. This tool was last updated about 5 years ago in Galaxy except for some changes to make the tool compatible with specific servers.

More importantly, it seems the underlying tool is no longer supported by Illumina, and I see several issues with “wes” as a keyword that seem very close to the result one would expect if the config file was missing a flag (although to be clear: I expected different config file values based on that flag, not a distinct flag itself, and I didn’t see that, see my test history below). Maybe there was a bug in the original tool?

Resources:

I don’t have more good advice from here…

I guess you could explore the original tool, how it works, possibly use it off line, and possibly update the Galaxy wrapper or submit a bug to the Galaxy dev repo and see if this can be addressed at that level, if the underlying tool checks out Ok as expected (providing your example of the issue). Then the wrapper could be adjusted to better match how the underlying tool is working.

Not a great answer, but it looks like this tool is deprecated (?). If I am wrong about any of this, please correct me! :slight_smile:

5

Thank you for your help. I tried install Manta and ran locally, and the results are different from what I get from Galaxy. I guess I should just submit a bug to the Galaxy dev repo then.

6

Yes, if you confirmed the bug, please submit the error. You’ll notice how others report the problems – explain a bit then share the example. If this is something you want to help with, state that in the Issue ticket, fork off a branch, install Planemo, and the development team can help with any questions or the review.

I think the tool needs more tool tests, too! I couldn’t get the other profiles to apply differences. I only found the tool at the EU server and the original university server here MISSISSIPPI - Galaxy Community Hub (disconnected, not sure why!).

Thanks for following up! :slight_smile: