If you run into a situation where a GC/MSD system is reporting "Host system not ready", check the injection source to be sure it is set to the desired headspace, valve or autosampler. The injection source can change in a method when there is an error or if the ALS (automatic liquid sampler) is disconnected.
The Host system error will be displayed on the GC front panel, shutting down the software will make it go away, this will be your indication that this is a method problem.
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