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The mocha tests are primarily what are used to ensure the job runner is functioning as intended. Since the release of 2.5.0, they have become out of date.

Per discussion with @stephenshank, we should make the number of processors requested configurable. Currently, revisioned code needs to be edited.

It appears that there may be an issue with FADE. It is the only method in our stats page that hasn't had a completed job in over a week.

Currently, if the process cannot connect to a redis server, a cryptic message occurs. We should check for the redis service in server.js and report an error if no connection can be made.

When using the FUBAR model on Datamonkey, I want to get the overall non-synonymous substitution rate and synonymous substitution rate of the sequence. In other models, this can usually be obtained from the log file. But in the FUBAR model, the log file is empty in most cases and there is no information.(empty file).

I have tried a sequence, which log file is empty in all models.
Some sequences are empty for the FUBAR model and normal for other models.

I am not sure if this is a bug, or a problem with my sequence?

Or is there any other way to get the overall non-synonymous and synonymous substitution rate of the FUBAR model?

If a job excessively prints to standard out, it will cause the application to fail due to flooding redis' pub/sub channel. We should put in place a mechanism inside of the node application to protect the pub/sub channel from excessive standard output.

When HyPhy lacks a specified keyword argument, it does not use the default value for non-required keywords, and prompts instead of exits for either required or non-required keywords.

Desired behavior would be to use the default value for non-required arguments, and exit with a notice when a required argument is missing.

Rarely, and when there are many jobs in queue, datamonkey-js-server will report qstat.stdout as undefined. We should have an exception handler for this case.

/home/datamonkey/datamonkey-js-test/lib/jobqueue.js:43
  qstat.stdout.on("data", function(data) {
               ^

TypeError: Cannot read property 'on' of undefined
    at returnJobInfo (/home/datamonkey/datamonkey-js-test/lib/jobqueue.js:43:16)
    at /home/datamonkey/datamonkey-js-test/lib/jobqueue.js:113:7
    at ChildProcess.exithandler (child_process.js:264:7)
    at emitTwo (events.js:125:13)
    at ChildProcess.emit (events.js:213:7)
    at maybeClose (internal/child_process.js:927:16)
    at Socket.stream.socket.on (internal/child_process.js:348:11)
    at emitOne (events.js:115:13)
    at Socket.emit (events.js:210:7)
    at Pipe._handle.close [as _onclose] (net.js:557:12)
events.js:182
      throw er; // Unhandled 'error' event

10|datamon | warn: gard : 5c275f798e810357458ad9dc : script error : {"error":"unable to read results file. empty html file","type":"script error","stderr":"--------------------------------------------------------------------------\nThere are not enough slots available in the system to satisfy the 48 slots\nthat were requested by the application:\n /home/datamonkey/datamonkey-js-server/production/app/gard/../../.hyphy_gard_version2_3_11/HYPHYMPI\n\nEither request fewer slots for your application, or make more slots available\nfor use.\n--------------------------------------------------------------------------\n","progress":"","stdout":"(echo /home/datamonkey/datamonkey-js-server/production/app/gard/output/5c275f798e810357458ad9dc; echo 010010; echo 3; echo 4; echo /home/datamonkey/datamonkey-js-server/production/app/gard/output/5c275f798e810357458ad9dc.GARD) | mpirun -np 48 /home/datamonkey/datamonkey-js-server/production/app/gard/../../.hyphy_gard_version2_3_11/HYPHYMPI LIBPATH=/home/datamonkey/datamonkey-js-server/production/app/gard/../../.hyphy_gard_version2_3_11/res/ /home/datamonkey/datamonkey-js-server/production/app/gard/../../.hyphy_gard_version2_3_11/res//TemplateBatchFiles/GARD.bf\n"}

Hi,
I haven't been able to pass through the MEME queue for 5 days. Using alignment that works fine using all other tools and runs immediately. Status is submitted, but waiting for ticket number. Tried multiple times on multiple days. Does this tool have a much longer queue?
Thanks!