I have a server that runs Pixelmon 1.8.9 4.2.5 , after putting sponge (mod) plugins to the mods folder I receive this :
10.06 03:27:02 [Multicraft] Received start command
10.06 03:27:02 [Multicraft] Loading server properties
10.06 03:27:02 [Multicraft] Starting server!
10.06 03:27:02 [Multicraft] Loaded config for "Special: custom.jar"
10.06 03:27:02 [Multicraft] Updating eula.txt file
10.06 03:27:02 [Multicraft] Failed to obtain process information: NoSuchProcess no process found with pid 4161
10.06 03:27:03 [server] main/INFO [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.FMLServerTweaker
10.06 03:27:03 [server] main/INFO [LaunchWrapper]: Using primary tweak class name net.minecraftforge.fml.common.launcher.FMLServerTweaker
10.06 03:27:03 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLServerTweaker
10.06 03:27:04 [server] INFO 2016-06-10 03:27:04,486 WARN Disabling terminal, you're running in an unsupported environment.
10.06 03:27:04 [server] main/INFO [FML]: Forge Mod Loader version 11.15.1.1722 for Minecraft 1.8.9 loading
10.06 03:27:04 [server] main/INFO [FML]: Java is Java HotSpot 64-Bit Server VM, version 1.8.0_92, running on Linux:amd64:3.14.32-xxxx-grs-ipv6-64, installed at /usr/lib/jvm/jre1.8.0_92
10.06 03:27:05 [server] main/WARN [FML]: The coremod chylex.javacheck.Java8CheckerCoremod does not have a MCVersion annotation, it may cause issues with this version of Minecraft
10.06 03:27:05 [server] main/INFO [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.FMLInjectionAndSortingTweaker
10.06 03:27:05 [server] main/INFO [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.FMLDeobfTweaker
10.06 03:27:05 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLInjectionAndSortingTweaker
10.06 03:27:05 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLInjectionAndSortingTweaker
10.06 03:27:05 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.relauncher.CoreModManager$FMLPluginWrapper
10.06 03:27:06 [server] main/ERROR [FML]: FML appears to be missing any signature data. This is not a good thing
10.06 03:27:06 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.relauncher.CoreModManager$FMLPluginWrapper
10.06 03:27:06 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.relauncher.CoreModManager$FMLPluginWrapper
10.06 03:27:06 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.FMLDeobfTweaker
10.06 03:27:06 [server] main/INFO [LaunchWrapper]: Loading tweak class name net.minecraftforge.fml.common.launcher.TerminalTweaker
10.06 03:27:06 [server] main/INFO [LaunchWrapper]: Calling tweak class net.minecraftforge.fml.common.launcher.TerminalTweaker
10.06 03:27:07 [server] main/INFO [LaunchWrapper]: Launching wrapped minecraft {net.minecraft.server.MinecraftServer}
10.06 03:27:10 [server] Server thread/INFO Starting minecraft server version 1.8.9
10.06 03:27:10 [server] Server thread/INFO [FML]: MinecraftForge v11.15.1.1722 Initialized
10.06 03:27:10 [server] Server thread/INFO [FML]: Replaced 204 ore recipies
10.06 03:27:10 [server] Server thread/INFO [FML]: Found 0 mods from the command line. Injecting into mod discoverer
10.06 03:27:10 [server] Server thread/INFO [FML]: Searching /mods for mods
10.06 03:27:12 [server] Server thread/INFO [FML]: Forge Mod Loader has identified 4 mods to load
10.06 03:27:12 [server] Server thread/INFO [FML]: FML has found a non-mod file Nexus.jar in your mods directory. It will now be injected into your classpath. This could severe stability issues, it should be removed if possible.
10.06 03:27:12 [server] Server thread/INFO [FML]: Attempting connection with missing mods [mcp, FML, Forge, pixelmon] at CLIENT
10.06 03:27:12 [server] Server thread/INFO [FML]: Attempting connection with missing mods [mcp, FML, Forge, pixelmon] at SERVER
10.06 03:27:13 [server] Server thread/INFO [FML]: Processing ObjectHolder annotations
10.06 03:27:13 [server] Server thread/INFO [FML]: Found 384 ObjectHolder annotations
10.06 03:27:13 [server] Server thread/INFO [FML]: Identifying ItemStackHolder annotations
10.06 03:27:13 [server] Server thread/INFO [FML]: Found 0 ItemStackHolder annotations
10.06 03:27:13 [server] Server thread/INFO [FML]: Configured a dormant chunk cache size of 0
10.06 03:27:13 [server] Forge Version Check/INFO [ForgeVersionCheck]: [Forge] Starting version check at http://files.minecraftforge.net/maven/net/minecraftforge/forge/promotions_slim.json
10.06 03:27:13 [server] Forge Version Check/INFO [ForgeVersionCheck]: [Forge] Found status: UP_TO_DATE Target: null
10.06 03:27:18 [server] Server thread/INFO [Pixelmon]: Loading TM/HMs.
10.06 03:27:18 [server] Server thread/INFO [Pixelmon]: Extracting database.
10.06 03:27:18 [server] Server thread/INFO [Pixelmon]: Loading database driver.
10.06 03:27:18 [server] Server thread/INFO [Pixelmon]: Establishing connection.
10.06 03:27:21 [server] Server thread/INFO [FML]: Applying holder lookups
10.06 03:27:21 [server] Server thread/INFO [FML]: Holder lookups applied
10.06 03:27:21 [server] Server thread/INFO [FML]: Injecting itemstacks
10.06 03:27:21 [server] Server thread/INFO [FML]: Itemstack injection complete
10.06 03:27:21 [server] Server thread/INFO Loading properties
10.06 03:27:21 [server] Server thread/INFO Default game type: SURVIVAL
10.06 03:27:21 [server] Server thread/INFO Generating keypair
10.06 03:27:21 [server] Server thread/INFO Starting Minecraft server on 37.187.136.112:25651
10.06 03:27:21 [server] Server thread/INFO Using epoll channel type
10.06 03:27:22 [server] Server thread/INFO [Pixelmon]: Registering shop items.
10.06 03:27:22 [server] Server thread/INFO [Pixelmon]: Registering NPCs.
10.06 03:27:22 [server] Server thread/INFO [Pixelmon]: Registering structures.
10.06 03:27:23 [server] Server thread/INFO [Pixelmon]: Registering drops.
10.06 03:27:23 [server] Server thread/INFO [Pixelmon]: Registering entity spawns.
10.06 03:27:25 [server] Server thread/INFO [FML]: Injecting itemstacks
10.06 03:27:25 [server] Server thread/INFO [FML]: Itemstack injection complete
10.06 03:27:25 [server] Server thread/INFO [FML]: Forge Mod Loader has successfully loaded 4 mods
10.06 03:27:25 [server] Server thread/INFO Preparing level "world"
10.06 03:27:25 [server] Server thread/INFO [FML]: Injecting existing block and item data into this server instance
10.06 03:27:25 [server] Server thread/INFO [FML]: Applying holder lookups
10.06 03:27:25 [server] Server thread/INFO [FML]: Holder lookups applied
10.06 03:27:25 [server] Server thread/INFO [FML]: Loading dimension 0 (world) (net.minecraft.server.dedicated.DedicatedServer@6f014bec)
10.06 03:27:25 [server] Server thread/INFO [FML]: Loading dimension 1 (world) (net.minecraft.server.dedicated.DedicatedServer@6f014bec)
10.06 03:27:25 [server] Server thread/INFO [FML]: Loading dimension -1 (world) (net.minecraft.server.dedicated.DedicatedServer@6f014bec)
10.06 03:27:25 [server] Server thread/INFO Preparing start region for level 0
10.06 03:27:26 [server] Startup Done (1.005s)! For help, type "help" or "?"
I assume that it's all about the "FML has found a non-mod file Nexus.jar in your mods directory. It will now be injected into your classpath. This could severe stability issues, it should be removed if possible."
Also I'm sure that I have downloaded the right version of Nexus for forge
For the sake of the test I only put Nexus . Any help is really appreciated