Question: Error running multi-input workflow after upgrade
1
jdv • 20 wrote:
After upgrading a local Galaxy instance to 16.10 (from 16.01), I now get an error trying to start a workflow with multiple input files. This happens even with a newly-created barebones testing workflow. The steps taken are:
- Select workflow to run
- Select multiple linked datasets for forward and reverse reads
- Select "Send results to new history: Yes"
- Click "Run Workflow"
A red error window is presented to the user with the following:
The server could not complete the request. Please contact the Galaxy Team if this error persists. "Uncaught exception in exposed API method:"
{
"new_history_name": "test_multi_",
"history_id": null,
"replacement_params": {},
"parameters": {
"0": {
"input": {
"values": [
{
"src": "hda",
"keep": false,
"hid": 1,
"id": "f730cea376070f95",
"name": "695_S12_L001_R1_001.fastq"
},
{
"src": "hda",
"keep": false,
"hid": 19,
"id": "5a3cb0004e7923b9",
"name": "trimmed_synced_sync.1.fq"
}
],
"batch": true
}
},
"1": {
"input": {
"values": [
{
"src": "hda",
"keep": false,
"hid": 2,
"id": "a4d69f1b7b4142ae",
"name": "695_S12_L001_R2_001.fastq"
},
{
"src": "hda",
"keep": false,
"hid": 20,
"id": "895e6d700409e1fc",
"name": "trimmed_synced_sync.2.fq"
}
],
"batch": true
}
},
"2": {
"library|type": "paired",
"pvalue": "0.01",
"min_overlap": "10",
"max_assembly_length": "0",
"min_assembly_length": "50",
"min_trim_length": "1",
"quality_threshold": "0",
"max_uncalled_base": "1.0",
"cap": "40",
"test_method": "1",
"empirical_freqs": "false",
"nbase": "false",
"score_method": "2",
"outputs": [
"assembled",
"report"
]
}
},
"parameters_normalized": true,
"batch": true
}
and I find this in the log:
galaxy.web.framework.decorators ERROR 2017-01-26 15:58:39,356 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/share/home/galaxy/galaxy/lib/galaxy/web/framework/decorators.py", line 282, in decorator
rval = func( self, trans, *args, **kwargs )
File "/share/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 478, in invoke
run_configs = build_workflow_run_configs(trans, workflow, payload)
File "/share/home/galaxy/galaxy/lib/galaxy/workflow/run_request.py", line 224, in build_workflow_run_configs
history = _get_target_history(trans, workflow, payload, expanded_param_keys, index)
File "/share/home/galaxy/galaxy/lib/galaxy/workflow/run_request.py", line 191, in _get_target_history
nh_name = '%s on %s and %s' % ( nh_name, ', '.join( ids[ 0:-1 ] ), ids[ -1 ] )
TypeError: sequence item 0: expected string, int found
It looks to me like a problem building the new history names, but I'm not sure. Any help would be appreciated. I had to clear out a cache directory to get DRMAA working after the upgrade, and I'm not sure if this is caused by a similar problem.
Jeremy