Hello everyone
I observed an issue when flagstat is incorporated in a workflow in which
the BAM file it works on is also used by another program (generate
pileup for instance) and is NOT the input dataset (generated by sam to
bam within the workflow).
I tested it with the local job runner and with TORQUE (with the pbs
scheduler and Maui).
- With the local job runner, it works just fine
- With TORQUE I get the following error message:
pbs_submit failed, PBS error 15033: No free connections
Surprisingly, other non-linear workflows work fine. I only observed this
error with flagstat. Moreover, when flagstat is in a linear workflow, it
works fine too. Ad if it is non-linear but the input dataset is the bam
file flagstat works on, it works fine too.
Please find attached one of the test workflow where I found the error.
The input dataset is a sam file.
Any clue?
Cheers,
LA
{
"a_galaxy_workflow": "true",
"annotation": "to see if it fails if not forked",
"format-version": "0.1",
"name": "test flagstat",
"steps": {
"0": {
"annotation": "",
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "Input Dataset"
}
],
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 200
},
"tool_errors": null,
"tool_id": null,
"tool_state": "{\"name\": \"Input Dataset\"}",
"tool_version": null,
"type": "data_input",
"user_outputs": []
},
"1": {
"annotation": "",
"id": 1,
"input_connections": {
"source|input1": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"name": "SAM-to-BAM",
"outputs": [
{
"name": "output1",
"type": "bam"
}
],
"position": {
"left": 274.5,
"top": 307
},
"tool_errors": null,
"tool_id": "sam_to_bam",
"tool_state": "{\"source\": \"{\\\"index_source\\\":
\\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\",
\"__page__\": 0}",
"tool_version": "1.1.1",
"type": "tool",
"user_outputs": []
},
"2": {
"annotation": "",
"id": 2,
"input_connections": {
"input1": {
"id": 1,
"output_name": "output1"
}
},
"inputs": [],
"name": "flagstat",
"outputs": [
{
"name": "output1",
"type": "txt"
}
],
"position": {
"left": 396.5,
"top": 445
},
"tool_errors": null,
"tool_id": "samtools_flagstat",
"tool_state": "{\"__page__\": 0, \"input1\": \"null\"}",
"tool_version": "1.0.0",
"type": "tool",
"user_outputs": []
},
"3": {
"annotation": "",
"id": 3,
"input_connections": {
"refOrHistory|input1": {
"id": 1,
"output_name": "output1"
}
},
"inputs": [],
"name": "Generate pileup",
"outputs": [
{
"name": "output1",
"type": "tabular"
}
],
"position": {
"left": 519,
"top": 340
},
"tool_errors": null,
"tool_id": "sam_pileup",
"tool_state": "{\"__page__\": 0, \"c\": \"{\\\"consensus\\\":
\\\"no\\\", \\\"__current_case__\\\": 0}\", \"indels\": \"\\\"no\\\"\",
\"refOrHistory\": \"{\\\"input1\\\": null, \\\"reference\\\": \\\"indexed\\\",
\\\"__current_case__\\\": 0}\", \"lastCol\": \"\\\"no\\\"\", \"mapCap\":
\"\\\"60\\\"\"}",
"tool_version": "1.1.1",
"type": "tool",
"user_outputs": []
}
}
}___________________________________________________________
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