Bug #682
closedpost processing amplitude correction fails
0%
Description
http://amilab16.scripps.edu/myami/processing/checkAppionJob.php?expId=7486&jobId=220
Here's the output from Appion
refine78_10jun17p26.appionsub.log:
... Running Appion version 'r14103'EMAN: proc3d /ami/exdata/appion/10apr15a/recon/emanrecon8/threed.9a.mrc
/ami/exdata/appion/ ... 784ff8a2.spi spidersingle
EMAN 1.9 Cluster ($Date: 2009/02/18 05:12:22 $).
Run 'proc3d help' for detailed help.
Original image : 480x480x480 Mean=-0.000339 Sigma=0.979 Min=-6.33 Max=10.3
Sampling : 1 A/pixel Origin = 0,0,0
Final image : 480x480x480 Mean=-0.000339 Sigma=0.979
Sampling : 1 A/pixel Origin = 0,0,0
[vol]784ff8a2
[outvol]out_784ff8a2
[scatter]/opt/appion/appionlib/data/ampcor5.spi
x99=480 ; box size in pixels
x98=4.6 ; filter limit in angstroms
x80=2.0 ; pixel size
[applyfen]/opt/appion/appionlib/applyfen
SPIDER: spider bat/spi @enhance_edit
... completed in 39.7 sec
calculating dimensions...
Traceback (most recent call last):
File "/opt/appion/bin/postProc.py", line 300, in ?
postProc.start()
File "/opt/appion/bin/postProc.py", line 207, in start
apDisplay.printError("amplitude correction failed")
File "/var/tmp/appion-2.0-6_rc1-root/opt/appion/appionlib/apDisplay.py", line 56, in printError
Exception:
- FATAL ERROR ***
amplitude correction failed
Updated by Anna-Clare Milazzo over 14 years ago
- Assignee set to Neil Voss
Sorry! I accidentally filed this under Leginon instead of Appion
Updated by Neil Voss over 14 years ago
- Status changed from New to Assigned
- Assignee changed from Neil Voss to Anna-Clare Milazzo
Try it again, I cannot determine why it failed.
Updated by Anna-Clare Milazzo over 14 years ago
I tried it again-- this time on emanrecon5 instead of emanrecon8 on the unfiltered hk97 data set and I still get the same error trying to correct with the GROEL sax data.
EMAN: proc3d /ami/exdata/appion/10apr15a/recon/emanrecon5/threed.9a.mrc/ami/exdata/appion/ ... b2306530.spi spidersingle
EMAN 1.9 Cluster ($Date: 2009/02/18 05:12:22 $).
Run 'proc3d help' for detailed help.
Original image : 480x480x480 Mean=1.8e-09 Sigma=1 Min=-6.54 Max=10.7
Sampling : 1 A/pixel Origin = -240,-240,-240
Final image : 480x480x480 Mean=1.8e-09 Sigma=1
Sampling : 1 A/pixel Origin = -240,-240,-240
[vol]b2306530
[outvol]out_b2306530
[scatter]/usr/lib64/python2.4/site-packages/appionlib/data/ampcor5.spi
x99=480 ; box size in pixels
x98=4.6 ; filter limit in angstroms
x80=2.0 ; pixel size
[applyfen]/usr/lib64/python2.4/site-packages/appionlib/applyfen
SPIDER: spider bat/spi @enhance_edit
... completed in 34.23 sec
calculating dimensions...
Traceback (most recent call last):
File "/opt/appion/bin/postProc.py", line 306, in ?
postProc.start()
File "/opt/appion/bin/postProc.py", line 213, in start
apDisplay.printError("amplitude correction failed")
File "/usr/lib64/python2.4/site-packages/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:
- FATAL ERROR ***
amplitude correction failed
Updated by Neil Voss over 14 years ago
- Status changed from Assigned to In Code Review
- Assignee changed from Anna-Clare Milazzo to Amber Herold
- Target version set to Appion/Leginon 2.1.0
- Affected Version changed from Appion/Leginon 2.0.1 to Pre-2.0
- Show in known bugs set to Yes
Updated by Amber Herold over 14 years ago
- Status changed from In Code Review to In Test
Updated by Amber Herold over 14 years ago
- Assignee changed from Amber Herold to Anna-Clare Milazzo
Updated by Eric Hou over 14 years ago
- Assignee changed from Anna-Clare Milazzo to Dmitry Lyumkis
Updated by Dmitry Lyumkis over 14 years ago
- Status changed from In Test to Closed
I'm filing this as passed, because it works with my version of Appion. However, when I test with betamyamiweb and it prepends the appion wrapper, the function fails. Some environmental variables are incorrectly set.
Updated by Amber Herold over 12 years ago
- Status changed from Closed to Assigned
- Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
Dmitry, can you be more specific about what environmental varialbles are incorrect?
I have not been able to run this successfully.
Updated by Dmitry Lyumkis over 12 years ago
can you give me write permissions on a folder that you want to test on, and send me the command
Updated by Amber Herold over 12 years ago
Here is an example:
/opt/myamisnap/bin/appion postProc.py --reconiterid=94 -s zz07jul25b -f /ami/data15/appion/zz07jul25b/recon/xmipp_recon46/Xmipp_results/recon_11nov09p19_it008_vol001.mrc --amp=ampcor5.spi --maxfilt=4.6 --apix=1.63 --res=10.01 --sym=c7 --median=2 --zoom=1.0 --contour=2.0 --lp=5.01 --norm --rundir=/ami/data15/appion/zz07jul25b/recon/xmipp_recon46/Xmipp_results/postproc/refine94_12apr16o49 --runname=refine94_12apr16o49 --projectid=303 --expId=8556 --jobtype=postproc
Updated by Amber Herold over 12 years ago
- Assignee changed from Dmitry Lyumkis to Amber Herold
Dmitry's works because his python path includes .../myami/appion
Updated by Amber Herold over 12 years ago
- Category changed from Python scripting to Installation
Updated by Amber Herold over 10 years ago
- Status changed from Assigned to Closed
- Affected Version changed from Pre-2.0 to Appion/Leginon 2.2.0