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": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9",
"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!
