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

We are not Sponge, go to their forums for support with it.