pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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Error in a single job SimpleMulti_LoadSegmentedObjects, project #37

Closed ewiger closed 8 years ago

ewiger commented 8 years ago

Project: DorisPop/IndividualExperiments/MPlex/160119-DorisFISHMtestcycle01eluted01. Name of breaking CP module is SimpleMulti_LoadSegmentedObjects. Happens on loading 160119-DorisFISHMtest-cycle01eluted01_C09_T0001F006L01A01Z01C01.png in

Error message says Could not unambiguously find corresponding image of other dataset. Please set more stringent filters.

Opening log file:  /cluster/home/biol/yyauhen/java.log.18886

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                    R2013a (8.1.0.604) 64-bit (glnxa64)
                             February 15, 2013

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/cluster/home/biol/yyauhen/iBRAIN/startup.m: randomizing rand initial state
/cluster/home/biol/yyauhen/iBRAIN/startup.m: 48 CPUs detected, using 1 threads
>> CPCluster - 10:26:58: Starting CPCluster
CPCluster - 10:26:58:   batchfile = /BIOL/sonas/biol_uzh_pelkmans_s4/Data/Users/DorisPop/IndividualExperiments/MPlex/160119-DorisFISHMtestcycle01eluted01/BATCH/Batch_data.mat
CPCluster - 10:26:58:   clusterfile = /BIOL/sonas/biol_uzh_pelkmans_s4/Data/Users/DorisPop/IndividualExperiments/MPlex/160119-DorisFISHMtestcycle01eluted01/BATCH/Batch_258_to_259.mat

filepathsep =

/

Ignoring custom project code support. Path does not exist: /BIOL/sonas/biol_uzh_pelkmans_s4/Data/Users/DorisPop/IndividualExperiments/MPlex/160119-DorisFISHMtestcycle01eluted01/LIB/MATLAB
CPCluster - 10:27:08: Analyzing image set 258 (max threads = 1)
CPCluster - 10:27:08:   01: LoadImages 
CPCluster - 10:27:10:     Image set 258 = 160119-DorisFISHMtest-cycle01eluted01_C09_T0001F006L01A01Z01C01.png
CPCluster - 10:27:10:   02: IlluminationCorrectionPelkmans 
Applying illumination correction on channel number: 1
CPCluster - 10:27:12:   03: IlluminationCorrectionPelkmans 
Applying illumination correction on channel number: 2
CPCluster - 10:27:14:   04: IlluminationCorrectionPelkmans 
Applying illumination correction on channel number: 3
CPCluster - 10:27:17:   05: SimpleMulti_LoadSegmentedObjects 
Batch Error: SimpleMulti_LoadSegmentedObjects Error using SimpleMulti_LoadSegmentedObjects>getFileNameViaReferenceFile (line 475)
Could not unambiguously find corresponding image of other dataset. Please set more stringent filters.
Error using SimpleMulti_LoadSegmentedObjects>getFileNameViaReferenceFile (line
475)
Could not unambiguously find corresponding image of other dataset. Please set
more stringent filters.

Error in SimpleMulti_LoadSegmentedObjects>getFileNameViaReferenceFile (line
475)
    error('Could not unambiguously find corresponding image of other dataset.
    Please set more stringent filters.');

Error in SimpleMulti_LoadSegmentedObjects (line 136)
[strCorrespondingImage_trans, couldFindSameSite_image,
strCorrespondingSegmentation_trans, couldFindSameSite_segmentation,
strCorrespondingSegmentationSecondary_trans, couldFindSameSite_segmentation_
Error in CPCluster (line 39)
                handles = feval(ModuleName,handles);
GitMotz commented 8 years ago

Pipeline runs, but the module assignes wrongly the segmentation, despite the fact that the number of images and sites are equal in input and exp on which the pipeline is used. Batch is in L:\Data\Users\DorisPop\IndividualExperiments\MPlex\160118-DorisFISHMtestcycle01

segmentationnotaligend

dorispgithub commented 8 years ago

I commented above, somehow ended up being logged as DorisB. Experiment in question is found in my files. DorisP

tstoeger commented 8 years ago

Doris and I just figured out the source of the problem. The source of the problem is neither related to iBrain or the module, but experimental.