BiG-SCAPE job submission failed

usegalaxy.eu support
1

Hi guys,
i’m working on a large dataset of .gbk files that i would like to analyze using Big-SCAPE. In particular, these are files from a previous AntiSMASH prediction (a total of 13000 files from 880 bacterial genomes). I’ve already uploaded the files through Galaxy API and collected in a dataset to be used as input for the tool. However, i receive an alert that says that the server could not complete the request. I attached you the error for completness.
Also, in the job information i’ve noticed in the Tool standard error the phrase: “Error: Input GenBank files should not have spaces in their path as hmmscan cannot process them properly (‘too many arguments’).” As these files are from the AntiSMSH output i do not understand where this error came…
Does anyone have some suggestions? Thank you for your responses!

The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.

"history_id": "def8b1aa791796d6",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bigscape/bigscape/1.1.9+galaxy2",
"tool_version": "1.1.9+galaxy2",
"inputs": {
    "inputdir": {
        "batch": false,
        "product": false,
        "values": [
            {
                "id": "ec6ab951019b4e85",
                "src": "hdca",
                "map_over_type": null
            }
        ]
    },
    "mibig|is_select": "yes",
    "mibig|mibig": "--mibig",
    "use_label|is_select": "no",
    "pfam_dir": {
        "batch": false,
        "product": false,
        "values": [
            {
                "id": "4838ba20a6d86765b3e11d7ca27970d4",
                "src": "hda",
                "map_over_type": null
            }
        ]
    },
    "verbose": true,
    "log": true,
    "include_singletons": false,
    "domain_overlap_cutoff": "0.1",
    "min_big_size": "0",
    "mix": false,
    "no_classify": false,
    "banned_classes": null,
    "cutoff_0|cutoffs": "0.3",
    "clans_off": false,
    "clan_cutoff|is_select": "no",
    "hybrids_off": false,
    "mode": "glocal",
    "anchor|is_select": "no",
    "force_hmmscan": false,
    "list|is_select": "no"
}

}

2

Welcome, @Elia_Soriato

The error is reporting a problem in the path to an input file, not a problem internal to the file itself.

If you click on the i-icon for one of the red dataset’s for the job output, and scroll down to the command line in the logs, you may be able to spot where the problem is and make an adjustment to avoid that space. Renaming the file? You can do that as part of a workflow if you are streaming the tools.

Please give that a review and let us know if we can help more. See the banner at the top of this forum for how to share your work. Thanks! :slight_smile:

3

Thank you very much! The issue was indeed related to the collection’s naming. After changing it without underscores, everything worked perfectly. Thanks again!

1 Like
4

Great, thanks for letting us know what worked, @Elia_Soriato

Hoping things go smoother for you from here :slight_smile: