It happens when you run a conversion on an old (pre-2.4) alignments set. I just tried it now using the new codebase and an old (c. 2021) alignments file/vid pair.
It updates the alignments file first, then runs the conversion, failing on every frame.
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Setting Faceswap backend to NVIDIA
04/21/2024 13:38:33 INFO Log level set to: INFO
04/21/2024 13:38:39 INFO Reading alignments from: '\\B450M\face_vidslib\-removed-\file_01_alignments.fsa'
04/21/2024 13:38:39 INFO Updating alignments file to version 2.4
04/21/2024 13:38:39 INFO Writing alignments to: '\\B450M\face_vidslib\-removed-\file_01_alignments.fsa'
04/21/2024 13:38:41 INFO Loading Model from Phaze_A plugin...
04/21/2024 13:38:41 INFO Config item: 'freeze_layers' has been updated from '['visual']' to '['keras_encoder']'
04/21/2024 13:38:41 INFO Using configuration saved in state file
04/21/2024 13:38:42 INFO Mixed precision compatibility check (mixed_float16): OK\nYour GPU will likely run quickly with dtype policy mixed_float16 as it has compute capability of at least 7.0. Your GPU: NVIDIA GeForce RTX 3060, compute capability 8.6
04/21/2024 13:38:47 INFO Loaded model from disk: 'D:\sample_data\models\_Phaze-A\-removed-\phaze_a.h5'
04/21/2024 13:38:48 INFO Loading Writer from Ffmpeg plugin...
04/21/2024 13:38:48 INFO Outputting to: '\\B550m\d\face_sample_data\video_src\vidout\deepfakes\phaze_a\-removed-\file_01_converted.mkv'
04/21/2024 13:38:48 INFO Loading Mask from Mask_Blend plugin...
04/21/2024 13:38:48 INFO Loading Color from Avg_Color plugin...
04/21/2024 13:38:48 INFO Loading Scaling from Sharpen plugin...
No alignment found for file_01_000001.mkv, skipping
No alignment found for file_01_000002.mkv, skipping
.. etc
So with some recent discoveries I figured I would run the mask update script I wrote yesterday to batch them all, and that threw a ton of similar errors:
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Setting Faceswap backend to NVIDIA
04/21/2024 13:57:06 INFO Log level set to: INFO
04/21/2024 13:57:10 INFO Reading alignments from: '\\B450M\face_vidslib\-removed-\file_01_alignments.fsa'
04/21/2024 13:57:10 INFO Loading Mask from Bisenet_Fp plugin...
04/21/2024 13:57:10 INFO Initializing BiSeNet - Face Parsing (Mask)...
04/21/2024 13:57:14 INFO Initialized BiSeNet - Face Parsing (Mask) with batchsize of 12
04/21/2024 13:57:14 INFO Generating masks
04/21/2024 13:57:14 WARNING Skipping frame not in alignments file: 'file_01_000001.mkv'
04/21/2024 13:57:14 WARNING Skipping frame not in alignments file: 'file_01_000002.mkv'
04/21/2024 13:57:14 WARNING Skipping frame not in alignments file: 'file_01_000003.mkv'
04/21/2024 13:57:14 WARNING Skipping frame not in alignments file: 'file_01_000004.mkv'
So I loaded the alignments and video into the Manual tool, and it all looked fine and worked as expected. The alignments were visible and correct. I made a simple change to one face (to enable the Save button) and saved it. Ran the mask update script and got the very same errors, 'Skipping frame not in alignments file'. Short of re-extracting I don't know what else to do in order to resurrect these older alignments.