--dir="C:\188kartikbranch\WorkFlowManager\bin\Debug\SkylineRunner" --in="C:\188kartikbranch\WorkFlowManager\TestData\BioTherapeutic\docs\MasterDataBioThera.sky" --import-all-files="C:\Users\conspai\AppData\Local\Temp\1wid24pd" --exp-method-instrument="Waters Xevo TQ" --tran-predict-ce="Waters Xevo" --exp-method-type=scheduled --exp-order-by-mz --exp-template="C:\188kartikbranch\WorkFlowManager\TestData\BioTherapeutic\docs\template.exp"  --exp-run-length=10 --exp-file="C:\Users\conspai\AppData\Local\Temp\biw5zqm5\OptimizeCe_105Trans.exp" --refine-max-transition-peak-rank=6 --refine-min-peak-found-ratio=0.1 --tran-product-ion-types="y,b"  --exp-optimizing="ce"  --out="C:\188kartikbranch\WorkFlowManager\TestOutput\4pmrmnrd\OptCE.sky" --exp-strategy=Buckets --exp-max-trans=40 --refine-missing-results --refine-max-precursor-only

Opening file...
File MasterDataBioThera.sky opened.
Document unchanged
Transition Settings -- Filter > Ion types changed to "y, b"
Settings > Transition Settings -- Filter > Ion types changed from "p, y, b" to "y, b"
Removed: 23 tran

Adding results...
1. C:\Users\conspai\AppData\Local\Temp\1wid24pd\StepB-FixedCE-ScheduleRT.raw
Adding results...
2. C:\Users\conspai\AppData\Local\Temp\1wid24pd\StepB-FixedCE-ScheduleRT2.raw

Joining file C:\188kartikbranch\WorkFlowManager\TestData\BioTherapeutic\docs\MasterDataBioThera.skyd
100% - Joining file C:\188kartikbranch\WorkFlowManager\TestData\BioTherapeutic\docs\StepB-FixedCE-ScheduleRT2_1974866032.raw.skyd
Updating peak statistics
Refining document...
Refined targets
Advanced refinement settings > Min peak found ratio is "0.1"
Advanced refinement settings > Max precursor peak only is True
Advanced refinement settings > Max transition peak rank is "6"
Advanced refinement settings > Remove nodes missing results is True
Removed: 1 pep, 16 prec, 378 tran
Saving file...
File OptCE.sky saved.
Error: The file C:\Users\conspai\AppData\Local\Temp\biw5zqm5\OptimizeCe_105Trans.exp could not be saved.  Check that the specified file directory exists and is writeable.
Failed to schedule the following peptides with the current settings:

R.HLHFTLVK.D [34, 41] - 42 transitions
R.DYYFALAHTVR.D [50, 60] - 42 transitions
K.ARPEFTLPVHFYGR.V [192, 205] - 42 transitions
R.VLYPNDNFFEGK.E [278, 289] - 42 transitions
R.HLQIIYEINQR.F [399, 409] - 42 transitions
K.DFYELEPHK.F [470, 478] - 42 transitions
K.VFADYEEYVK.C [773, 782] - 42 transitions

Check max concurrent transitions count and optimization step count.