.tiff input not recognised
Hi,
I want to run this pipeline on a .tiff file (not .tif) and it seems the first process (scaling) doesn't even start.
My current pipeline version on branch refactoring:
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$ git rev-parse HEAD
e348ab6311ef120a4544acd6e2b158763a1ad63a
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$This is the content of params.yml for reference:
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$ ls
assets bin conf main.nf modules nextflow.config params.yml readme.md results scripts testdata work
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$ cat params.yml
video_path:
- ../Valeria/NGLUT250227_hab3.tiff
skip_scaling: false
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$Here is the error I get if I run the pipeline; it seems it looks for a .tif file but can't find it.
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$ module load Nextflow/24.10.4 Miniforge3/24.1.2-0
(base) [torchia@login2 calcium_imaging_pipeline_with_nextflow]$ nextflow run main.nf -profile embl_hd -params-file params.yml
Nextflow 25.04.6 is available - Please consider updating your version to it
N E X T F L O W ~ version 24.10.4
Launching `main.nf` [nasty_nightingale] DSL2 - revision: fbbbab3005
Motion correction parameters path: /g/gross/Sofia/nextflow_examples/calcium_imaging_pipeline_with_nextflow/./assets/motion_correction.json
executor > slurm (1)
[04/9963c8] CAIMAN_MOTION_CORRECTION:SCALE (1) [ 0%] 0 of 1
[- ] CAIMAN_MOTION_CORRECTION:BACKGROUNDSUBTRACTION -
[- ] CAIMAN_MOTION_CORRECTION:REMOVEBLACKFRAMES -
[- ] CAIMAN_MOTION_CORRECTION:MOTIONCORRECTION -
ERROR ~ Error executing process > 'CAIMAN_MOTION_CORRECTION:SCALE (1)'
Caused by:
Missing output file(s) `NGLUT250227_hab3_scaled.tif` expected by process `CAIMAN_MOTION_CORRECTION:SCALE (1)`
Command executed:
ImageJ-linux64 --headless --console -macro scale_video.ijm NGLUT250227_hab3.tiff
Command exit status:
0
Command output:
same_frame_extended(@641)
at loci.plugins.in.ImporterPrompter.promptMain(ImporterPrompter.java:132)
at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:79)
at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:476)
at loci.plugins.in.ImportProcess.step(ImportProcess.java:772)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:243)
at ij.IJ.runPlugIn(IJ.java:204)
at ij.IJ.runPlugIn(IJ.java:193)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:524)
executor > slurm (1)
[04/9963c8] CAIMAN_MOTION_CORRECTION:SCALE (1) [100%] 1 of 1, failed: 1 ✘
[- ] CAIMAN_MOTION_CORRECTION:BACKGROUNDSUBTRACTION -
[- ] CAIMAN_MOTION_CORRECTION:REMOVEBLACKFRAMES -
[- ] CAIMAN_MOTION_CORRECTION:MOTIONCORRECTION -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'CAIMAN_MOTION_CORRECTION:SCALE (1)'
Caused by:
Missing output file(s) `NGLUT250227_hab3_scaled.tif` expected by process `CAIMAN_MOTION_CORRECTION:SCALE (1)`
Command executed:
ImageJ-linux64 --headless --console -macro scale_video.ijm NGLUT250227_hab3.tiff
Command exit status:
0
Command output:
same_frame_extended(@641)
at loci.plugins.in.ImporterPrompter.promptMain(ImporterPrompter.java:132)
at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:79)
at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:476)
at loci.plugins.in.ImportProcess.step(ImportProcess.java:772)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:243)
at ij.IJ.runPlugIn(IJ.java:204)
at ij.IJ.runPlugIn(IJ.java:193)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:524)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:97)
at ij.IJ.runUserPlugIn(IJ.java:243)
mmand at ij.IJ.runPlugIn(IJ.java:204)
OpenJDat ij.IJ.runPlugIn(IJ.java:193)
OpenJDat ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:555)
Jul 14at ij.io.Opener.openUsingHandleExtraFileTypes(Opener.java:407)
WARNINat ij.io.Opener.openImage(Opener.java:386)
Jul 14at ij.io.Opener.openImage(Opener.java:241)
WARNINat ij.io.Opener.open(Opener.java:104)
at ij.IJ.open(IJ.java:1936)
rk dirat ij.macro.Functions.open(Functions.java:3044)
/g/groat ij.macro.Functions.doFunction(Functions.java:159)
at ij.macro.Interpreter.doStatement(Interpreter.java:281)
ntaineat ij.macro.Interpreter.doStatements(Interpreter.java:267)
/scratat ij.macro.Interpreter.run(Interpreter.java:163)
at ij.macro.Interpreter.run(Interpreter.java:93)
p: youat ij.macro.Interpreter.run(Interpreter.java:107)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:162)
- Checat ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:146)
at ij.IJ.runMacroFile(IJ.java:171)
at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:1165)
at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:1161)
at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:1095)
at net.imagej.legacy.IJ1Helper.runMacroFile(IJ1Helper.java:1161)
at net.imagej.legacy.LegacyCommandline$Macro.handle(LegacyCommandline.java:185)
at org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:99)
at org.scijava.AbstractGateway.launch(AbstractGateway.java:103)
at net.imagej.Main.main(Main.java:55)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:87)
Command error:
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Jul 14, 2025 10:09:38 AM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Jul 14, 2025 10:09:38 AM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
Work dir:
/g/gross/Sofia/nextflow_examples/calcium_imaging_pipeline_with_nextflow/work/04/9963c8f24f8ea70dce36291593faa5
Container:
/scratch/tabaro/nextflow/apptainer/fiji-fiji-20220415.img
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for details
Thank you so much for your support!
Sofia