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Re: [proteowizard-support] MSConvert Email From Windows To Mac.
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From: Chambers, M. <mat...@gm...> - 2021-03-02 22:18:52
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Can you create a new file in that folder? (Right Click -> New -> Text file). On 3/2/2021 3:47 PM, Kassim Santone wrote: > Hi, > > So I went into the properties of my Desktop folder and unchecked the Read-Only option. Same exact error though. > > On Mon, Mar 1, 2021 at 7:00 PM Nick Shulman <nicksh@u.washington.edu <mailto:nicksh@u.washington.edu>> wrote: > > That looks like the sort of error that you would get if your user did not have write permission on the folder "C:\Desktop". > > In this case "unable to open file" means "unable to open a stream for writing". > > -- Nick > > On Mon, Mar 1, 2021 at 1:57 PM Kassim Santone <san...@gm... <mailto:san...@gm...>> wrote: > > I'm using the 64-bit version. I just put my entire Desktop out of the "Kassim Santone" folder (now it's just /Users/Desktop) but > now I am getting this error where it's saying the .mzML file does not exist but I'm a little confused because isn't the .mzML file > what we're creating, so shouldn't it not exist until it's done anyway? > > On Mon, Mar 1, 2021 at 10:54 AM Chambers, Matthew <mat...@gm... <mailto:mat...@gm...>> wrote: > > I agree with Nick that it's odd that a file reading an mzML file would care about the path to the file that it's reading. > Actually a direct conversion from WIFF to mzML shouldn't include a path to the mzML file, but it will include a path to the > WIFF and WIFF.SCAN. A 2nd generation mzML (converted from WIFF to mzML then converted from mzML to another mzML, perhaps with > different filter settings) would have a path to the 1st generation mzML though. > > The location attributes in my mzML do have backslashes but they also have 3 slashes like "file:///D:\test\Thermo". So maybe > Nick's right about that. What version of msconvert are you using? > > On 2/27/2021 3:50 PM, Nick Shulman wrote: >> When you use msconvert to create a .mzML file, that .mzML file will always contain some XML elements which describe what file >> it was converted from. >> I was not aware of any tools that actually pay attention to that part of the .mzML file, but it sounds like you have one. >> >> It might be that your tool is complaining about the fact that "file://C:\Users\Kassim Santone\Desktop" has a space in it, and >> a space is not usually a valid character to have in the middle of a URL. If that's the case, then I would expect you to be >> able to work around this problem by putting your wiff file to a folder on your virtual machine where the path does not have a >> space on it, and running msconvert on the file in that location. >> >> If that does not fix the problem, then you might have to actually edit your .mzML file using a text editor. >> >> NOTE: if you are going to use a text editor to modify a .mzML file, you need to make sure it was created with the "Write >> index" option turned off (or the "--noindex" option specified if you are using the commandline msconvert.exe). The index is a >> block of text at the end of the file which has numbers in it referring to actual byte locations within the file, so if you >> make any edits to the file, the numbers in the index will become invalid. >> >> The thing that I would recommend changing using the text editor is to find where it says: >> "file://C:\Users\Kassim Santone\Desktop" >> and change it to: >> "file:///C:/Users/Kassim%20Santone/Desktop" >> Your software might be complaining about the backslashes, or the space, or might want three slashes at the beginning of the >> URL instead of two. (I am not sure whether these things are violations of the URL standards, but it's possible). >> >> If your mzML file is very large, you might not be able to edit it using an ordinary text editor. On Windows, I use a program >> called "emeditor" to edit very large text files. >> >> Hope this helps, and let us know what you find out. >> -- Nick >> >> On Sat, Feb 27, 2021 at 10:49 AM Kassim Santone <san...@gm... <mailto:san...@gm...>> wrote: >> >> Hi, >> >> I am currently using a Mac and I tried to use MSConvert on a Windows virtual machine (I sent my .wiff and .wiff.scan >> files to my email and opened them on the Windows computer). I then convert the .wiff and .wiff.scan files into an .mzML >> file with MSConvert (this was done on the directory on my Windows machine C:\Users\Kassim Santone\Desktop, after sending >> it back the .mzML was on the directory on my Mac's machine /Users/kassimsantone/Desktop but it seemed when I ran a target >> from an open-source library called OpenMS (link included) with the target called OpenSwathWorkflow I get this error in my >> IDE. >> >> <While loading >> '/Users/kassimsantone/Desktop/hroest_K120808_Strep0%PlasmaBiolRepl1_R01_SW-Strep-0%-Plasma-Biol-Repl1.mzML.gz': Ill >> formed absolute or relative sourceFile path: file://C:\Users\Kassim Santone\Desktop> occurred 2 times >> >> Process finished with exit code 3 >> >> So apparently the .mzML file on my Mac still somehow has reference to the desktop directory (ie file://C:\Users\Kassim >> Santone\Desktop) and is trying to use this sourceFile path unsuccessfully. Why is the .mzML still have some metadata on >> it's directory location from Windows. How can I fix this so I can use the .mzML file? >> >> Thanks. >> _______________________________________________ >> proteowizard-support mailing list >> pro...@li... <mailto:pro...@li...> >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support >> <https://lists.sourceforge.net/lists/listinfo/proteowizard-support> >> >> >> >> _______________________________________________ >> proteowizard-support mailing list >> pro...@li... <mailto:pro...@li...> >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support <https://lists.sourceforge.net/lists/listinfo/proteowizard-support> > > _______________________________________________ > proteowizard-support mailing list > pro...@li... <mailto:pro...@li...> > https://lists.sourceforge.net/lists/listinfo/proteowizard-support <https://lists.sourceforge.net/lists/listinfo/proteowizard-support> > |
