Remove misleading "No such file or directory" syntax errors from output files

[DavidHuber-NOAA]

Bugzilla #1369

This is a followup to NOAA-EMC/global-workflow#1252.

Details from bugzilla:

From NCO SPA:

In the output logs for gfs/gdas/enkfgdas there are hundres of instances of "No such file or directory" messages 
printed out across many different tasks, which makes it more difficult to troubleshoot production failures.
Please work towards removing all related syntax errors from the output logs

A list of tasks from the 12z cycle found with these messages:
...
gfs_atmos_tropcy_qc_reloc_12

---

Additional notes from noaa-emc/global-workflow#1252:
NOAA-EMC/global-workflow#1252 (comment)

There are also similar messages coming from the TC tracker and genesis applications. See respectively the following:

/scratch1/NCEPDEV/da/Henry.Winterbottom/work/global-workflow/COMROOT/x001_gfsv17_issue_1252/logs/2021122100/gfstracker.log

/scratch1/NCEPDEV/da/Henry.Winterbottom/work/global-workflow/COMROOT/x001_gfsv17_issue_1252/logs/2021122100/gfsgenesis.log

For the CI C96_atm3DVar, those are the remaining No such file or directory instances.

Messages are being generated by ush/extrkr_gfs.sh lines 726, 1284, and 1285.