Re: [galaxy-user] Flagstat crashes in non-linear workflows with TORQUE

3 Jun 2011


      Louise-Amélie Schmitt wrote:
...
Le 06/04/2011 13:57, Nate Coraor a écrit :
...
Louise-Amélie Schmitt wrote:
...
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
Hi,
This can most likely be fixed by increasing the value of NCONNECTS in
the TORQUE source, in src/include/libpbs.h, and recompiling on your
TORQUE server.  I haven't seen a problem after increasing the value to
20.
--nate
Hi,
Sorry this is old but I tried recompiling torque after setting the
NCONNECTS to 20 and the issue's still there.
But there's more: It doesn't affect only flagstat but other
non-linear workflows. One of the two jobs that are submitted when
their "father" stopped running triggers the same error:
PBS error 15033: No free connections
Did you recompile both the client and the server?  I am not sure which
needs it, possibly both.
...
And the best part is that it works fine sometimes. But when it
crashes, it's always the same job that crashes.
Does anyone have a clue?
Cheers,
L-A
...
...
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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