Question: tophat tool stalled
gravatar for franziska.denk
3.5 years ago by
European Union
franziska.denk0 wrote:

Hi there, 

I was a bit impatient earlier in the day and terminated tophat on the main galaxy tool while it was still loading its instructions to the history. It now refuses to run and is telling me "job submission failed" with the following code:

    "tool_id": "",
    "tool_version": "0.9",
    "inputs": {
        "singlePaired|sPaired": "paired",
        "singlePaired|input1": {
            "batch": true,
            "values": [
                    "src": "hda",
                    "hid": 819,
                    "id": "bbd44e69cb8906b5d1d4d2067081b8a7",
                    "name": "R40_TG_GAGTGG_L002_R1_001.fastq"
                    "src": "hda",
                    "hid": 823,
                    "id": "bbd44e69cb8906b5ffbe636f837d260f",
                    "name": "R52_TG_TGACCA_L001_R1_001.fastq"
                    "src": "hda",
                    "hid": 825,
                    "id": "bbd44e69cb8906b5f153478c47b43a83",
                    "name": "R53_TG_ACTTGA_L001_R1_001.fastq"
        "singlePaired|input2": {
            "batch": true,
            "values": [
                    "src": "hda",
                    "hid": 820,
                    "id": "bbd44e69cb8906b5b84963048f7fe5e5",
                    "name": "R40_TG_GAGTGG_L002_R2_001.fastq"
                    "src": "hda",
                    "hid": 824,
                    "id": "bbd44e69cb8906b5218a75b9b05e73df",
                    "name": "R52_TG_TGACCA_L001_R2_001.fastq"
                    "src": "hda",
                    "hid": 826,
                    "id": "bbd44e69cb8906b5a6b41f8d16eb90ac",
                    "name": "R53_TG_ACTTGA_L001_R2_001.fastq"
        "singlePaired|mate_inner_distance": "300",
        "singlePaired|mate_std_dev": "20",
        "singlePaired|report_discordant_pairs": "Yes",
        "refGenomeSource|genomeSource": "indexed",
        "refGenomeSource|index": "rn5",
        "params|settingsType": "full",
        "params|read_realign_edit_dist": "1000",
        "params|read_edit_dist": "2",
        "params|library_type": "fr-unstranded",
        "params|read_mismatches": "2",
        "params|bowtie_n": "No",
        "params|anchor_length": "8",
        "params|splice_mismatches": "0",
        "params|min_intron_length": "70",
        "params|max_intron_length": "500000",
        "params|indel_search|allow_indel_search": "Yes",
        "params|indel_search|max_insertion_length": "3",
        "params|indel_search|max_deletion_length": "3",
        "params|max_multihits": "2",
        "params|min_segment_intron": "50",
        "params|max_segment_intron": "500000",
        "params|seg_mismatches": "2",
        "params|seg_length": "25",
        "params|output_unmapped": "false",
        "params|own_junctions|use_junctions": "No",
        "params|coverage_search|use_search": "No",
        "params|microexon_search": "No",
        "params|fusion_search|do_search": "No",
        "params|bowtie2_settings|b2_settings": "No",
        "readGroup|specReadGroup": "no",
        "__job_resource|__job_resource__select": "no"

I think what might be happening is that I still have some incomplete jobs stuck somewhere that I cannot access. Would you be able to check for me "behind the scenes" and delete whatever might be pending and could be causing the problems?

Thank you! 

software error • 857 views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson25k • written 3.5 years ago by franziska.denk0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I went in and looked at your account. It appears that prior runs were terminated/perm deleted and new runs are both executing and queued. So, all is as expected. Was there anything I missed that is still problematic?

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k

Hi Jen,

Ah yes it appears to have fixed itself! Thanks for checking so quickly.

Best wishes, Franziska

ADD REPLYlink written 3.5 years ago by franziska.denk0
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