>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
>
>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

> 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
>

>> 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": []
>>          }
>>      }
>> }