Batmass-IO binaries for Thermo support and/or Thermo native libraries not found

[namine007]

I am trying to run my thermo fisher RAW files on MSF like usual. I am doing this on a daily basis. Starting last week it doesn't work any more. I have tried running on several PC and many versions. Now only FPv18/MSFv3.5/Philv4.4.0 works. The error I got is:

Batmass-IO binaries for Thermo support and/or Thermo native libraries not found
There are corrupted files. Please remove those files and re-start the task.
Checking spectral files...
T:\180\XXXX.raw: Scans = 0
Process 'MSFragger' finished, exit code: 1
Process returned non-zero exit code, stopping

This file worked on one PC but not the other so I'm not sure if this is a MSF problem/ raw data file problem.
I have also redownloaded MSF3.7 and checked the ext which should contain thermo doc and it does.

Any thought what's going on here?
Thanks! Any comment would be appreciated!

[fcyu]

Can you open cmd.exe, go to ext/thermo, run BatmassIoThermoServer.exe, and send us the screenshot?

Thanks,

Fengchao

[namine007]

I'm not sure how to run the exe file. I can open it on notepad:
<?xml version="1.0" encoding="utf-8"?> <configuration> <startup> <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6.1" /> </startup> <runtime> <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"> <dependentAssembly> <assemblyIdentity name="System.Collections.Concurrent" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.0.11.0" newVersion="4.0.11.0" /> </dependentAssembly> </assemblyBinding> <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"> <dependentAssembly> <assemblyIdentity name="System.Collections" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.0.11.0" newVersion="4.0.11.0" /> </dependentAssembly> </assemblyBinding> <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"> <dependentAssembly> <assemblyIdentity name="System.ComponentModel" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.0.1.0" newVersion="4.0.1.0" /> 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culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.0.1.0" newVersion="4.0.1.0" /> </dependentAssembly> </assemblyBinding> <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"> <dependentAssembly> <assemblyIdentity name="System.Threading.Timer" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.0.1.0" newVersion="4.0.1.0" /> </dependentAssembly> </assemblyBinding> <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"> <dependentAssembly> <assemblyIdentity name="System.ValueTuple" publicKeyToken="cc7b13ffcd2ddd51" culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.0.2.0" newVersion="4.0.2.0" /> </dependentAssembly> </assemblyBinding> <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1"> <dependentAssembly> <assemblyIdentity name="System.Xml.ReaderWriter" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" /> <bindingRedirect oldVersion="0.0.0.0-4.1.1.0" newVersion="4.1.1.0" /> </dependentAssembly> 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If I copy and paste the code on command prompt, it tells me the syntax of the command is incorrect.

[fcyu]

I'm not sure how to run the exe file. I can open it on notepad:

You should not open it on notepad. I think you need to let your IT department to help you.

Best,

Fengchao

[namine007]

BatmassIoThermoServer.exe is a config file BatmassIoThermoServer.exe.config. and removing the .config portion of the extension does not execute the application.

[fcyu]

There are both BatmassIoThermoServer.exe.config and BatmassIoThermoServer.exe:

Following is what it looks like when running BatmassIoThermoServer.exe in command line environment (cmd.exe)

You can reproduce it by 1) open cmd.exe; and 2) run the command similar to the above screenshot. If you have difficult to run it, please contact your IT department. I don't think we can troubleshoot remotely if you could not run the command.

Best,

Fengchao

[fcyu]

Oh, there is a possibility that your Windows hides the file extension, which is the default setting. Then, the BatmassIoThermoServer.exe what you saw is actually BatmassIoThermoServer.exe.config. If so, you need to find the BatmassIoThermoServer file.

Best,

Fengchao

[namine007]

Hi Fengchao,
There is no BatmassIoThermoServer.exe in MSF 3.6 or 3.7. We found it in MSF 3.5 and searched my files using Fragpipe v18 MSF3.5, Ionquant 1.8.10, Philodopher 4.7.0 and it worked. Thanks for the help!

Best,
Jeanne

[fcyu]

Hi Jeanne,

I am 100% sure that you messed up the files because there have been thousands of users downloaded the version 3.6 and 3.7, but no one have ever complained that there was no BatmassIoThermoServer.exe. Also, if you take a closer look at my previous reply, you will find that the BatmassIoThermoServer.exe I was using is located in G:\bin\MSFragger-3.7\ext\thermo\.

We found it in MSF 3.5 and searched my files using Fragpipe v18 MSF3.5, Ionquant 1.8.10, Philodopher 4.7.0 and it worked.

The BatmassIoThermoServer.exe in version 3.5 is not fully compatibly with version 3.6 and 3.7 because we fixed some bugs and made some changes. We suggest you use the least version (3.7).

In a word, please download MSFragger again and start from scratch.

Best,

Fengchao

[namine007]

Hi Fengchao,

As suggested, I have redownload and installed Fragpipe 19.1, MSF 3.7, IonQuant 1.8.10, Philosopher 4.8.1. Still doesn't work for our thermo RAW files. Here is the full error code.

MSFragger version MSFragger-3.7
Batmass-IO version 1.28.9
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 32 GB memory
Checking database...
Failed in checking T:\197\197_Hela_100ng.raw. Will ignore it.
Batmass-IO binaries for Thermo support and/or Thermo native libraries not found
There are corrupted files. Please remove those files and re-start the task.
Checking spectral files...
T:\197\197_Hela_100ng.raw: Scans = 0
Process 'MSFragger' finished, exit code: 1
Process returned non-zero exit code, stopping

Thanks!

[fcyu]

Just to make it clear, you actually didn't do what I suggested in the first reply after rounds of conversation: #255 (comment)

If you have difficulty to troubleshoot, please convert your raw files to mzML according to our tutorial: https://fragpipe.nesvilab.org/docs/tutorial_convert.html

Best,

Fengchao

[bdrown]

I was troubleshooting a similar issue and found this thread so I thought I would chime in. CiscoSecureEndpoint detected BatmassIoThermoServer.exe as a possible trojan during the download/install of MSFragger and quarantined it. With no BatmasIO, I saw similar behavior as described above. This is more of an issue for Cisco and my IT, but @namine007 may have been dealing with antiviral software.