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": [] } } } ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: