Error processing aligned tilt series from IMOD

[Laura Caccianini]

Hi everyone, I was trying to process a tilt series, pre-processed with WARP and aligned in IMOD, and I got this error:

System.Exception: System.Exception: Could not successfully
read file within the specified number of attempts.
at Warp.Image.FromFilePatient(Int32 attempts, Int32 mswait,
String path, int2 headerlessSliceDims, Int32 headerlessOffset,
Type headerlessType, Int32 layer, Stream stream) in
D:\Dev\warp2 WarpLib\mage, c:line 337
at
WarpWorker.Program.LoadAndPrepareGainReference(String
path, Boolean flipX, Boolean flipY, Boolean transpose) in
D:\Dev)warp2\Warp Worker\Program, cs: line 369
at WarpWorker.Program.Main(String] args) in
D:\Dev warp2\WarpWorker\Program, c:line 137
at Warp.WorkerWrapper.GetSuccessStatus0 in
D:\Dev\warp2/WarpLib\WorkerWrapper.cs:line96
at Warp. WorkerWrapper,LoadGainRef(String path, Boolean
flipX, Boolean flipY, Boolean transpose, String defectsPath) in
D;\Dev\warp2 WarpLib \WorkerWrapper.cs:line 136
at
Warp.MainWindow,«>c_DisplayClass64_1.<«ButtonStartProc
essing_OnClick>b__0>d.MoveNextnin
DA\Dev\warp2) Warp Main Window,xaml.cs:line O
- End of stack trace from previous location where exception
was thrown --.
System.Runtime ExceptionServices.ExceptionDispatchinfo.Thro
WO
at
System.Runtime.Compiler5ervices. TaskAwaiter HandleNonSucc
essAndDebuggerNotification(Task task)
at
Warp. Main Window. « ButtonStartProcessing_OnClick-d__64.M
oveNext© in Da_Dev warp2\Warp\MainWindow.xaml.cs.line
1958
End of stack trace from previous location where exception
was thrown -
af
System.Runtime.ExceptionServices.ExceptionDispatchinfo.Thro
WOl
at
System.Windows.Threading.ExceptionWrapper.InternalRealCa
"(Delegate callback, Object args, Int32 numArgs)
System.Windows.Threading.ExceptionWrapper.TryCatchWhent
Object source, Delegate callback, Object args, Int32 numArgs,
Delegate catchHandler)
at Warp.WorkerWrapper.GetSuccessStatusDin
DADev warp2\WarpLib WorkerWrapper. cs. line 96
at Warp.WorkerWrapperLoadGainRef(String path, Boolean
flipX, Boolean flipY, Boolean transpose, String defectsPath) in
DADevwarp2 WarpLib\WorkerWrapper.cs:line136
Warp.Main Window, « > c DisplayClass64_1.«≤ ButtonStartProc
essina OnClick- b. _O» d.MoveNext0 in
DA\Dewwarp2\Warp\MainWindow.xaml,cs:lineQ
- End of stack trace from previous location where exception
was thrown-
43
System.Runtime ExceptionServices,ExceptionDispatchinfo.Thro
at
System.Runtime.CompilerServices,TaskAwaiter.HandleNonSucc
essAndDebuggerNotification(Task task)
at
Warp.Main Window. « ButtonStartProcessing OnClick>d64.M
oveNext0 in D'\Dev warp2 Warp\MainWindow.xaml.cs:line
1958
_- End of stack trace from previous location where exception
at
System. Runtime, ExceptionServices. ExceptionDispatchinfo. Thro
WO
aT
System.Windows.Threading.ExceptionWrapper.InternalRealCa
I (Delegate callback, Object args, Int32 numArgs)
at
System.Windows.Threading.ExceptionWrapper.TryCatchWhen(
Object source, Delegate caliback, Object args, Int32 numArgs,

Delegate catchHandler) 

I also tried processing a single tilt and I got this other error:

An error occurred while fitting the CTF. Likely reasons include:

- Insufficient read/write permissions in this folder.

- Too low defocus to yield more than one CTF peak in the processing range.

- Mismatch in gain reference and image dimensions.

The exception raised is:

System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException* was thrown.

at Warp.Image.get_HostData0 in D:\Dev\warp2\WarpLib\mage.cs:line 97

at Warp.Image..ctor(int3 dims, Boolean isft, Boolean iscomplex, Boolean ishalf) in D:\Dev\warp2\WarpLib

image.cs:line 245

at Warp.TiltSeries.<>c_DisplayClass115_0.<LoadMovieData>b_2(Int32 i) in DA\Dev/warp2\WarpLib

\TiltSeries.cs.line 7676

at Warp.Tools.Helper.ArrayOfFunction{T](Func"2 generator, Int32 n) in D:\Dev\warp2WarpLib\Tools\Helper.cs:line

768

at Warp.TiltSeries.LoadMovieData(ProcessingOptionsBase options, Movie(]& movies, Imaqe[]& movieData,

Boolean doOddEven, Image[]& movieDataOdd, Image[)& movieDataEven) in Di\Dev\warp2\WarpLib

\TiltSeries.cs:.line 7676

at Warp.TiltSeries.ProcessCTFSimultaneous(ProcessingOptionsMovieCTFoptions)inDA\Dev\warp2\WarpLib

\TiltSeries.cs.line 482

at Warp.MainWindow.<>C_DisplayClass103_0.<<ButtonProcessOneltemCTF_OnClick>b_0>d.MoveNextOinD:

\Dev\warp2\Warp\MainWindow.xaml.cs:line3008

I checked for dimensions mismatch in gain and image and they are the same size. I am processing data living on a NAS formatted on a Linux machine, but checked folder permissions and they seem ok. 

I am new to tomography data processing and I will appreciate any input. 

Thanks!

Laura

[Pranav Shah]

The path to a file (prbably gain ref? would be useful to know on which
step M dies) referenced in your *.source file is wrong. Manually edit
it so that it is right and try again.
Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

> --
> You received this message because you are subscribed to the Google Groups "Warp" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to warp-em+u...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/warp-em/810e74b4-916c-4489-9087-d9d9d1152bc2n%40googlegroups.com.

[Laura Caccianini]

Hi Pranav, thank you very much for your answer and apologies for the late reply.

I tried moving the Gain correction file in the folder where my raw tilts and the .mdoc files are but it did not solve the problem.

Also, why would WARP be ok with it in the first processing step, when Gain correcting and preparing the file to be fed to IMOD?

I tried to figure out why WARP was failing on the IMOD-aligned individual tilt processing. I checked that the size of Gain and tilts are the same (they are), I checked the folder permissions (they seem ok), and I tried allocating more RAM to Warp. When I allocate more RAM (I set the Priority to "Realtime" in the Task Manager) WARP seems to take a little more time before crushing. Do you have any thoughts on this?

I would be more than happy to provide you with any further info you might find useful.

Cheers,

Laura

[Digvijay Singh]

Hi Laura,

In addition to Pranav's suggestion, some more possibilities could be the mismatch between input tomo dimensions and input frames dimensions (e.g, 3838 by 3710 against input frames dimension of 3710 by 3838 if the |tilt-axis|~90 ). 

If the |tilt-axis|~90, then the dimensions of un-aligned tilt-series (.st file) and aligned tilt-series (.ali) are different as per IMOD's default conventions. 

HTH,

Digvijay

[Giulia Paris]

Hi everyone,

I’m jumping into this open discussion because I also got the same error described above.

I pre-processed my raw movies in Warp, then generated the tilt stack, which I aligned with aretomo. I the imported back the aligned tilt series in Warp and when trying to estimate the CTF for the aligned tilt series, I get the following error when “Process only this item’s CTF”:

Then :

- I checked the permissions and everything looks fine to me,

- I tried to adjust the defocus values, but nothing changed

- finally, the raw movies were already gain corrected, so I guess I can exclude errors with the gain reference?

And now I am out of ideas! If anyone has any suggestions, I would appreciate a lot!

Thank you in advance

Giulia