MSAmanda and Myrimatch do not work in latest SearchGUI Docker distribution

[MaxAlex]

On the newest version of the docker image on Biocontainers (quay.io/biocontainers/searchgui:4.0.33--h779adbc_0 found at https://biocontainers.pro/tools/searchgui), MS Amanda and Myrimatch are not executing correctly. Namely;

MS Amanda does not run; even trying to run the program with a command such as
docker run quay.io/biocontainers/searchgui:4.0.33--h779adbc_0 mono "/usr/local/share/searchgui-4.0.33-0/resources/MS Amanda/MSAmanda.exe"
gives the error
Cannot open assembly '/usr/local/share/searchgui-4.0.33-0/resources/MS Amanda/MSAmanda.exe': File does not contain a valid CIL image.

Myrimatch does run and executes a search, but does not produce a result file. Here is a sample terminal output:

Process #0 (db8229e54734) is starting.
MyriMatch 2.2.10165 (2016-11-7)
FreiCore 1.6.11103 (2017-7-14)
ProteoWizard MSData 3.0.11841 (2018-3-8)
ProteoWizard Proteome 3.0.11579 (2017-11-14)
Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari
Licensed under the Apache License, Version 2.0

Could not find the default configuration file (hard-coded defaults in use).
Reading "/data/K562_Analysis_miniSG_K562_searchGUI_analysis/human_UniProt_wDecoy.fasta"
Read 524922 proteins; 0.538816 seconds elapsed.
Reading spectra from file "/data/tempfiles/K562_Analysis_miniSG_K562_searchGUI_analysis/peak_lists/20100614_Velos1_TaGe_SA_K562_6.raw.mgf"
myrimatch: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.


Wed Jun 16 05:15:23 GMT 2021 MyriMatch finished for 20100614_Velos1_TaGe_SA_K562_6.raw.mgf (775.0 milliseconds).

Wed Jun 16 05:15:23 GMT 2021 Could not find MyriMatch result file for 20100614_Velos1_TaGe_SA_K562_6.raw.mgf.

Going back to an earlier version of the container (I tried quay.io/biocontainers/searchgui:4.0.4--h516909a_0) avoids these issues. The host machine executing the docker image is a standard Ubuntu 20:04 image on an AWS instance. I gather this is a problem with the docker packaging rather than searchGUI itself, so if that isn't maintained by the same folks please disregard this bug report.

Thanks!

[MaxAlex]

An addendum to the above; for reasons possibly unrelated, OMSSA also does not work in Docker images I've tried; this error occurs even in the 4.0.4 version which has a working MS Amanda and Myrimatch. (I forgot about this one since, IIRC, it hasn't worked since I started using SearchGUI.)

OMSSA fails with the message

"omssacl.cpp", line 216: Fatal: COMSSA::Run() - Unable to open blast library human_UniProt_wDecoy.fasta with error:NCBI C++ Exception:
    "/net/frosty/vol/export1/proteomics_alg/projects/omssa/c++/src/objtools/blast/seqdb_reader/seqdbalias.cpp", line 319: Error: ncbi::CSeqDBAliasNode::x_ResolveNames() - No alias or index file found for protein database [human_UniProt_wDecoy.fasta] in search path [/data/K562_Analysis_miniSG_K562_searchGUI_analysis::]

which may be related to an earlier, nonfatal error:

/usr/local/share/searchgui-4.0.4-0/resources/makeblastdb/linux/linux_64bit/makeblastdb: error while loading shared libraries: libbz2.so.1: cannot open shared object file: No such file or directory

Again, this is occurring at least for quay.io/biocontainers/searchgui:4.0.33--h779adbc_0 and :4.0.4--h516909a_0 , on the same Ubuntu 20.04 AWS instance host as the previous issue.

Thanks again.

[CarlosHorro]

Hi @MaxAlex ,

We have some hypothesis about the cause of these problems, but I'm quite surprised about the fact that they seemed to work in older versions.
Looking into this may require some time but I will try to do it.

Greetings,
Carlos

[CarlosHorro]

Hi @MaxAlex ,

I just wanted to clarify that we are working on this and we have found the cause of MsAmanda problem (they have moved their project to .NET core platform). A new version of SG application will be soon released with this fix, although the Docker container, conda package and Galaxy tool may require some time to be updated.

We will keep you updated about all other issues you reported.
Greetings,
Carlos

[MaxAlex]

Excellent, thanks! I look forward to the new version.

[CarlosHorro]

Hi @MaxAlex ,

Today a new version of SearchGUI application has been released solving MSAmanda problem. We will still need time to update the Conda package, Docker container and Galaxy tool to this last version.
Myrimatch and OMSSA bugs will also be fixed in those releases when they are available.

Greetings,
Carlos

[MaxAlex]

Thanks again!

Another question related to all of this; since Andromeda is typically supported on Windows only, would this be expected to work in the Docker image? I notice that it's available in the image, but it also results in an error when run.

[CarlosHorro]

Hi @MaxAlex ,

We have been trying to support Andromeda in Linux/MacOS using mono/dotnet for a long time, but it has not been possible due to different issues, so it is normal that it throws an error when trying to execute it into a container.

Greetings,
Carlos

[CarlosHorro]

Hi @MaxAlex ,

We have finally released new versions of SearchGUI (v4.0.41) and PeptideShaker (v2.0.33) Conda packages and Docker containers. The Galaxy tools are not ready yet, but I think you were more interested on the containers :-)

Greetings,
Carlos

[MaxAlex]

Thanks again for your hard work. Something might still not be right, though- now using the updated container, quay.io/biocontainers/searchgui:4.0.41--h779adbc_0, MS Amanda now throws a different error;

Failure processing application bundle.
Bundle header version compatibility check failed
A fatal error was encountered. Could not extract contents of the bundle

And Myrimatch also throws an error, also different from before;

myrimatch: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.

[CarlosHorro]

Hi @MaxAlex ,

Thank you very much for your highly valuable feedback, I was recently aware of the new Ms Amanda problem but I really thought that Myrimatch bugfix was working, so I must have missed something there too.
I will contact you again as soon as there are news about this all.

Greetings,
Carlos

[CarlosHorro]

Hi @MaxAlex ,

We have released new versions of SearchGUI and PeptideShaker Conda packages, Docker containers and Galaxy tools which must solve all previously commented issues.
Conda packages and Docker containers versions are:

• SearchGUI 4.0.41.1
• PeptideShaker 2.0.33

I hope they will work for you as expected.

Greetings,
Carlos

[MaxAlex]

I've just now gotten a chance to test the updated version; Myrimatch appears to work but MSAmanda searches are failing with a new error, namely

/usr/local/share/searchgui-4.0.41-1/resources/MS Amanda/linux/MSAmanda: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory

[CarlosHorro]

Hi @MaxAlex ,

Sorry for the inconveniences, I was aware of the possibility of that type of problem but I supposed it would happen in rare occasions... I guess I was wrong...
This one is a more complicated problem to solve... we will see what can be done.

Greetings,
Carlos

[CarlosHorro]

I've just now gotten a chance to test the updated version; Myrimatch appears to work but MSAmanda searches are failing with a new error, namely

/usr/local/share/searchgui-4.0.41-1/resources/MS Amanda/linux/MSAmanda: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory

Hi @MaxAlex , I'm sorry to say that the cause of this error is out of our hands as it is a bioconda-related issue when creating the Conda package (and using the last MS Amanda version). It could be solved if there was a MS Amanda Conda package, but there isn't..
So, I'm afraid that the only way to bypass this issue is to use an older version of SearchGUI (with an older version of MS Amanda). The last one with MS Amanda depending on the previous framework is SG 4.0.22.

Greetings,
Carlos