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Immortalin / peptide-shaker

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Entire folder with databases gets wiped when importing results #52

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
I have a folder d:/databases which contains all my fasta files.
A few weeks ago when using peptideshaker I already noticed the folder was 
suddenly wiped, but I was unable to reproduce it.
This morning it occured again. To reproduce the problem, I made a folder on 
another drive containing the mgf files, fasta files, etc needed for a searchGUI 
search.
But when I import these results in peptideshaker, I still see all my fasta 
files (restored from a backup) in the d:/database folder vanishing.
So I repeated it again, and kept looking at the folder, and I saw the fasta 
files disappear one by one!
It happens during the "importing sequences from...fasta" step.

> What is the expected output? What do you see instead?
Peptideshaker shouldn't even be looking in this folder, I never mentioned it in 
the searchGUI search.

> What version of the product are you using? On what operating system?
0.33.6. I updated peptideshaker this morning.

> Please provide any additional information below.
Very irritating problem. The first time I really lost all my fasta files.
And what's even stranger: I was only able to recover 30% of the files using 
recuva...

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).

Original issue reported on code.google.com by debock.p...@gmail.com on 9 Sep 2014 at 1:47

GoogleCodeExporter commented 9 years ago 
Hello and thank you for reporting this issue.

This is very weird, as you say, PeptideShaker should not be looking at this 
folder at all and in no case delete your files. We might have a clue on what 
went wrong. Can you do a simple check to confirm that we are pointing at the 
correct problem?

When editing the search settings in SearchGUI or PeptideShaker, in front of 
'Database (FASTA)', click 'Edit'; select any database and click 'Advanced' near 
the 'Decoy' button. Can you confirm that 'D:/database' is selected here? 
If so, a quick fix is to click browse and select an empty folder (like 
'D:/database/temp'). On our side, we will make sure that your files are not 
deleted in future versions, independent of the selected folder.

Sorry for the inconvenience,

Marc

Original comment by mvau...@gmail.com on 9 Sep 2014 at 2:30

GoogleCodeExporter commented 9 years ago 
Hi Marc,

d:/database was indeed selected in the advanced tab.

Thanks for the solution!
PJ

Original comment by debock.p...@gmail.com on 9 Sep 2014 at 2:33

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 9 Sep 2014 at 5:21

GoogleCodeExporter commented 9 years ago 
Hi again,
happy to hear that it worked. Thanks for reporting this, the bug will be fixed 
in the next release. We will keep the thread open until the fix has been 
released.
Best regards and don't hesitate to contact us again if you encounter any other 
problem,
Marc

Original comment by mvau...@gmail.com on 9 Sep 2014 at 6:59

GoogleCodeExporter commented 9 years ago 
A new version of PeptideShaker has been released where this issue is fixed.

Original comment by mvau...@gmail.com on 21 Sep 2014 at 4:29