Support request #158

Deconvolution fails after Upgrade to 3.0.2 (HuCore 4.4.0)

Added by Anonymous almost 7 years ago. Updated over 6 years ago.

Status:ClosedStart date:2013-07-05
Priority:HighDue date:
Assignee:Daniel% Done:


Category:Support Request
Target version:-


Hi HRM Team

We upgraded to core 4.4 and HRM 3.0.2 earlier this week and since then deconvolution with ICS and Imaris files fails without any meaningful error message. It says that it skips creating a log file. I attached the most recent email about a failed job, but I'm at a loss about what else to provide that is meaningful.

We tried downgrading, but this only worked to 3.0.1 and 4.3 since the database was upgraded and not backed up before.

Is there something I can set or collect to get more information about the jobs at hand, so I can debug this more clearly? I'm sorry I can't send more meaningful messages.

Thanks and kind regards,

This is a mail generated automatically by the Huygens Remote Manager.

Sorry, the processing of the image
tile exp_Series024.ics
has been terminated with an error.

Best regards,
Huygens Remote Manager

- HUYGENS ERROR REPORT (stderr) --------------

Skipping log file creation

Local time 2013-07-05 12:39:18
Error when processing template /huygens/data/j.m/huygens_src/.hrm_51d6a25509f2a.tcl
Local time 2013-07-05 12:39:20

- USER PARAMETERS -----------------------------------

These are the parameters you set in the HRM:

Image parameters:

number of channels:                  2
microscope type: single point confocal
numerical aperture: 1.4
objective type: oil
sample medium: liquid vectashield / 90-10 (v:v) glycerol - PBS ph 7.4
excitation wavelength: 488, 561
emission wavelength: 510, 585
pixel size: 60
z step size: 170
time interval: not set
pinhole size: 285.16, 285.16
point spread function: theoretical
aberration correction necessary: yes
perform aberration correction: no

Restoration parameters:

signal noise ratio:                  10, 10
background estimation: auto
number of iterations: 20
quality change stopping criterion: 0.1
deconvolution algorithm: cmle

Analysis parameters:

coloc analysis:                      no

- TEMPLATE -------------------------------------------

What follows is the Huygens Core template executed when the error occured:

info {title {Batch Processing template} version 2.2 templateName batch_2013-07-05_12-39-47 date {Fri Jul 5 12:39:47 CEST 2013}}
taskList {setEnv taskID:0}
setEnv {resultDir {/huygens/data/j.m/huygens_dst} perJobThreadCnt auto concurrentJobCnt 1 OMP_DYNAMIC 1 timeOut 10000 exportFormat {type ics multidir 0 cmode scale}}
taskID:0 {info {state readyToRun tag {setp Micr decon Decon} timeStartAbs 1373020787 timeOut 10000 userDefConfidence default} taskList {imgOpen setp adjbl cmle:0 cmle:1 previewGen:0 previewGen:1 previewGen:2 previewGen:3 previewGen:4 previewGen:5 previewGen:6 previewGen:7 previewGen:8 previewGen:9 previewGen:10 previewGen:11 imgSave} imgOpen {path {/huygens/data/j.m/huygens_src/tile exp_Series024.ics} series off index 0} setp {completeChanCnt 2 micr {confocal confocal} parState,micr {noMetaData noMetaData} s {0.06 0.06 0.17 *} parState,s {noMetaData noMetaData noMetaData default} iFacePrim 0.0 parState,iFacePrim default iFaceScnd 0.0 parState,iFaceScnd default pr {285.16 285.16} parState,pr {noMetaData noMetaData} imagingDir {upward upward} parState,imagingDir {noMetaData noMetaData} objQuality {good good} parState,objQuality {default default} pcnt {1 1} parState,pcnt {noMetaData noMetaData} ex {488 561} parState,ex {noMetaData noMetaData} em {510 585} parState,e
m {noMetaData noMetaData} exBeamFill {2.0 2.0} parState,exBeamFill {default default} ri {1.47 1.47} parState,ri {noMetaData noMetaData} ril {1.515 1.515} parState,ril {noMetaData noMetaData} na {1.4 1.4} parState,na {noMetaData noMetaData}} adjbl {enabled 0 ni 0} cmle:0 {q 0.1 brMode one it 20 bgMode auto bg 0 sn 10 blMode auto pad auto psfMode auto psfPath {} timeOut 36000 mode fast} cmle:1 {q 0.1 brMode one it 20 bgMode auto bg 0 sn 10 blMode auto pad auto psfMode auto psfPath {} timeOut 36000 mode fast} previewGen:0 {image raw destDir {/huygens/data/j.m/huygens_src/hrm_previews} destFile {tile exp_Series024.ics} type XYXZ size 400} previewGen:1 {image raw destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {tile exp_Series024.ics} type XYXZ size 400} previewGen:2 {image deconvolved destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics} type XYXZ size 400} previewGen:3 {image raw destDir {/huygens/data/j.
m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics.original} type orthoSlice size 400} previewGen:4 {image deconvolved destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics} type orthoSlice size 400} previewGen:5 {image deconvolved destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics.stack} type ZMovie size 400} previewGen:6 {image deconvolved destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics.tSeries} type timeMovie size 400} previewGen:7 {image deconvolved destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics.tSeries.sfp} type timeSFPMovie size 400} previewGen:8 {image raw destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics.original.sfp} type SFP size 400} previewGen:9 {image deconvolved destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hr
m.ics.sfp} type SFP size 400} previewGen:10 {destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics} type compareZStrips size 400} previewGen:11 {destDir {/huygens/data/j.m/huygens_dst/hrm_previews} destFile {51d6a25509f2a_hrm.ics} type compareTStrips size 400} imgSave {rootName {tile_exp_Series024_51d6a25509f2a_hrm}}}

- HUYGENS REPORT (stdout) --------------------

Running /usr/local/svi/bin/hucore.bin
HomePath predefined /usr/local/svi/
Looking for Tcl in /usr/local/svi/tcl/lib/tcl8.5...
Tcl version 8.5.10 type 2.
Huygens Core 4.4.0p4 initializing Compute Engine 4.4.0p4...
The system ID is 8b9b-e90d-03c9-a203.
Launching task 0 for client 0, ID: 0 on cpu group 0

- PROCESS DETAILS-------------------------------------

Your job started on 2013-07-05 12:39:24 and failed on 2013-07-05 12:39:47.
Job id: 51d6a25509f2a (pid 24173 on localhost)


#1 Updated by Daniel almost 7 years ago

  • Assignee set to Daniel
  • Priority changed from Normal to High

Hello Sabino,

If you provide me with an SSH connection I can try to assist you. Would that be possible?
You can contact me via e-mail to arrange the connection.

Could you please also let us know if the deconvolution jobs finish successfully for files the other file types?

Thank you,

#2 Updated by Daniel almost 7 years ago

  • Status changed from New to Closed

A restart of the Queue Manager (hrmd) solved the issue.

The installation was properly set up and the problem could not be reproduced after the QM restart.

#3 Updated by Niko over 6 years ago

  • % Done changed from 0 to 100

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