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": []
>         }
>     }
> }

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