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Bug #2249

closed

FindEM fails when filename size exceeds 76 characters

Added by Dmitry Lyumkis about 12 years ago. Updated about 12 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Julia Luciano
Category:
Python scripting
Target version:
-
Start date:
02/12/2013
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
No
Workaround:

Description

This was discovered by Julia when she was processing in session 12dec03f. The image filenames were too long, and the .dwn.mrc image that was created and fed into FindEM was not being read.

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 #1

Updated by Dmitry Lyumkis about 12 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Dmitry Lyumkis to Amber Herold

I put in a fix in apFindEM.py, which creates a soft link inside the directory using a random 10-letter filename, then feeds that link into FindEM. Everything else in the directory is the same.

The code was tested using a single, long micrograph in directory: /ami/exdata/appion/12dec03f/extract/test_Dmitry

Amber: please review code.

Julia: You should be able to use / test the fix tomorrow (February 13), when it gets updated on the nightly build. If you would like to test it on a single micrograph, you could use the command below (note that currently the --runname and --rundir options are set to --runname=test_fix, --rundir=/ami/exdata/appion/12dec03f/extract/test_fix)

/opt/myami-2.2/bin/appion templateCorrelator.py --projectid=377 --session=12dec03f --runname=test_fix --rundir=/ami/exdata/appion/12dec03f/extract/test_fix --no-rejects --no-wait --no-commit --continue --maxsize=0.05 --peaktype=centerofmass --maxthresh=0.8 --thresh=0.35 --median=2 --lowpass=15 --highpass=0 --planereg --bin=4 --diam=190 --pixlimit=2.0 --template-list=22,21 --range-list=0,180,10x0,180,10 --thread-findem --use-mirrors --expId=10743 -m 12dec03f_Prj377_Keap1-50ug-ml-thincarbon_i001_00054sq_v01_00002hl_v01_00002en.mrc

Otherwise, just make another jobfile and run the template correlator as usual.

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 #2

Updated by Amber Herold about 12 years ago

  • Status changed from In Code Review to Assigned
  • Assignee changed from Amber Herold to Sargis Dallakyan

I've reviewed and Merged the code to 2.2. I still need to do a merge to 2.2redux tomorrow.
Sargis, please update the Goby installation to this new revision, then assign this issue to Julia to Test.

Thanks!

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 #3

Updated by Sargis Dallakyan about 12 years ago

  • Status changed from Assigned to In Test
  • Assignee changed from Sargis Dallakyan to Julia Luciano
  • Affected Version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0

Thank you all. Installed this new revision on Goby head node and all work nodes:

[root@goby ~]# ./safadmin  rpm -Uvh --force http://goby.amigroup.scripps.edu/centos/5/extras/x86_64/RPMS/myami-2.2-750.x86_64.rpm

Assigning this issue to Julia to Test.

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 #4

Updated by Julia Luciano about 12 years ago

Hi All

I tested in a few micrographs with 81 characters and it all worked well.
Submitted a new jobfile in apFindEM.py and committed to the database, and it ran completely without failure.

Thanks!

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 #5

Updated by Dmitry Lyumkis about 12 years ago

  • Status changed from In Test to Closed
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