Error in file public data

[ypriverol]

This file has an error:

2021-03-07 23:42:01 INFO Started parsing MFA389.raw
2021-03-07 23:42:01 ERROR Error opening (ThermoFisher.CommonCore.RawFileReader.Facade.RawFileLoader) - MFA389.raw

http://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD014145/MFA389.raw

[caetera]

Hi @ypriverol,

The file was converted to mzML without any errors with the latest release version of TRFP (1.3.2) on Windows and Linux (Ubuntu 18.04.5, Mono 6.12). Could you provide more details how to reproduce the error?

[ypriverol]

It actually works. Apparently, mono 6 if you use symbolic links, it will not work. if the file you are trying to convert is a symbolic link to another file, it will not work on mono 6.

[bernt-matthias]

Is there a way to fix this? The Galaxy wrapper (actually any conda installation) suffers from the same problem since mono 6 is available. Still using a symlink seems very reasonable and handy.

I see the following ways to solve this (roughly ordered by my preference):

• an actual fix
• enforcing mono <6 in the bioconda recipe
• enforcing mono <6 in the Galaxy wrapper
• using a copy instead of a symlink

[caetera]

Hi @bernt-matthias

the actual fix should likely be issued by mono developers. I am not sure how to approach it from the TRFP side, any suggestions are welcome. I can only think of checking if we are on mono 6 and the input file is a symlink and try to fail with some sensible error or attempt to recover (copy the target file, "expand" the symlink). It sounds like quite an ugly fix to me.

[bernt-matthias]

Thanks for you efforts.

Then I would go for option 2 for now.

Could you open an issue at the mono repository? I

[bernt-matthias]

https://github.com/bernt-matthias/bioconda-recipes/pull/new/topic/trfp-mono

[caetera]

I will need to do a little bit of investigation to localize the problem a bit better before I can open the issue.

[caetera]

A small update. I am afraid it is not mono, since I could reproduce the same error on native Windows, i.e. if the file is a symlink the library from Thermo refuses to open it. Surprisingly, there is no obvious and platform independent way to get the target of a symlink from C#. I will keep looking into it.

[bernt-matthias]

Thanks for the update. Then its odd that it works for mono<5, or?

[caetera]

It is, I don't have any explanation for it