Hi,
Thanks for attaching the files. The main manifest files (manifest.f4m and manifest_v1.f4m) both have missing media elements. The child manifest (user1_209.f4m) seems to be intact but the bitrate shown is 0. Please try adding videoBitrates and audioBitrates parameters in the transcode command. You may refer to the EMS User Guide and API Definition documents for details on the transcode command. If it still fails, please send the relevant logs and the config.lua files.
Cheers,
Don