3v Running Log for JobId '2017.may17.b6c'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=177.8.106.218 (Wed May 17 12:41:03 2017)
  • waiting for system load (7.90) to calm down, total wait time: 5 min 29 sec (Wed May 17 12:41:03 2017)
  • waiting for system load (7.37) to calm down, total wait time: 9 min 47 sec (Wed May 17 12:46:32 2017)
  • waiting for system load (7.35) to calm down, total wait time: 14 min 3 sec (Wed May 17 12:50:51 2017)
  • waiting for system load (7.69) to calm down, total wait time: 19 min 3 sec (Wed May 17 12:55:07 2017)
  • waiting for system load (7.35) to calm down, total wait time: 23 min 19 sec (Wed May 17 13:00:07 2017)
  • waiting for system load (7.58) to calm down, total wait time: 28 min 4 sec (Wed May 17 13:04:23 2017)
  • waiting for system load (7.56) to calm down, total wait time: 32 min 46 sec (Wed May 17 13:09:08 2017)
  • waiting for system load (7.56) to calm down, total wait time: 37 min 29 sec (Wed May 17 13:13:50 2017)
  • waiting for system load (7.60) to calm down, total wait time: 42 min 16 sec (Wed May 17 13:18:33 2017)
  • waiting for system load (7.75) to calm down, total wait time: 47 min 24 sec (Wed May 17 13:23:21 2017)
  • waiting for system load (7.75) to calm down, total wait time: 52 min 32 sec (Wed May 17 13:28:28 2017)
  • waiting for system load (7.82) to calm down, total wait time: 57 min 49 sec (Wed May 17 13:33:36 2017)
  • running now (Wed May 17 13:38:54 2017)
  • downloading pdb file (Wed May 17 13:38:54 2017)
  • waiting for system load (7.85) to calm down, total wait time: 63 min 11 sec (Wed May 17 13:38:54 2017)
  • waiting for system load (7.80) to calm down, total wait time: 68 min 25 sec (Wed May 17 13:44:15 2017)
  • waiting for system load (7.96) to calm down, total wait time: 1 hr 14 min (Wed May 17 13:49:30 2017)
  • waiting for system load (7.58) to calm down, total wait time: 1 hr 19 min (Wed May 17 13:55:07 2017)
  • waiting for system load (7.82) to calm down, total wait time: 1 hr 24 min (Wed May 17 13:59:52 2017)
  • waiting for system load (7.93) to calm down, total wait time: 1 hr 30 min (Wed May 17 14:05:10 2017)
  • waiting for system load (7.99) to calm down, total wait time: 1 hr 35 min (Wed May 17 14:10:43 2017)
  • waiting for system load (7.80) to calm down, total wait time: 1 hr 41 min (Wed May 17 14:16:24 2017)
  • waiting for system load (7.38) to calm down, total wait time: 1 hr 45 min (Wed May 17 14:21:39 2017)
  • waiting for system load (6.74) to calm down, total wait time: 1 hr 48 min (Wed May 17 14:25:59 2017)
  • running now (Wed May 17 14:29:08 2017)
  • waiting for system load (6.46) to calm down, total wait time: 1 hr 51 min (Wed May 17 14:29:09 2017)
  • waiting for system load (6.49) to calm down, total wait time: 1 hr 54 min (Wed May 17 14:31:52 2017)
  • waiting for system load (6.39) to calm down, total wait time: 1 hr 56 min (Wed May 17 14:34:38 2017)
  • waiting for system load (5.97) to calm down, total wait time: 1 hr 58 min (Wed May 17 14:37:14 2017)
  • waiting for system load (6.01) to calm down, total wait time: 2 hr 0 min (Wed May 17 14:39:17 2017)
  • waiting for system load (6.01) to calm down, total wait time: 2 hr 2 min (Wed May 17 14:41:23 2017)
  • waiting for system load (5.81) to calm down, total wait time: 2 hr 4 min (Wed May 17 14:43:29 2017)
  • waiting for system load (5.89) to calm down, total wait time: 2 hr 6 min (Wed May 17 14:45:21 2017)
  • running now (Wed May 17 14:47:18 2017)
  • completed download of PDB id 3f1n (size: 476 k, 6023 lines) (Wed May 17 14:47:18 2017)
  • waiting for system load (5.82) to calm down, total wait time: 2 hr 8 min (Wed May 17 14:47:18 2017)
  • waiting for system load (5.99) to calm down, total wait time: 2 hr 10 min (Wed May 17 14:49:10 2017)
  • waiting for system load (5.85) to calm down, total wait time: 2 hr 12 min (Wed May 17 14:51:15 2017)
  • waiting for system load (3.93) to calm down, total wait time: 2 hr 12 min (Wed May 17 14:53:09 2017)
  • running now (Wed May 17 14:53:34 2017)
  • converting pdb into xyzr (Wed May 17 14:53:34 2017)
  • waiting for system load (3.58) to calm down, total wait time: 2 hr 13 min (Wed May 17 14:53:34 2017)
  • waiting for system load (3.70) to calm down, total wait time: 2 hr 13 min (Wed May 17 14:53:52 2017)
  • waiting for system load (3.79) to calm down, total wait time: 2 hr 13 min (Wed May 17 14:54:11 2017)
  • waiting for system load (3.85) to calm down, total wait time: 2 hr 14 min (Wed May 17 14:54:33 2017)
  • running now (Wed May 17 14:54:56 2017)
  • completed conversion of PDB file: 3f1n-2017.may17.b6c.pdb (size: 119k) (Wed May 17 14:54:59 2017)
  • converted 3800 atoms of 3800 atoms (Wed May 17 14:54:59 2017)
  • found 3800 atoms in pdb (Wed May 17 14:54:59 2017)
  • waiting for system load (3.90) to calm down, total wait time: 2 hr 14 min (Wed May 17 14:54:59 2017)
  • waiting for system load (4.01) to calm down, total wait time: 2 hr 15 min (Wed May 17 14:55:23 2017)
  • waiting for system load (4.01) to calm down, total wait time: 2 hr 15 min (Wed May 17 14:55:51 2017)
  • waiting for system load (4.16) to calm down, total wait time: 2 hr 16 min (Wed May 17 14:56:18 2017)
  • waiting for system load (4.46) to calm down, total wait time: 2 hr 16 min (Wed May 17 14:56:50 2017)
  • waiting for system load (4.88) to calm down, total wait time: 2 hr 17 min (Wed May 17 14:57:31 2017)
  • running now (Wed May 17 14:58:30 2017)
  • running 3v all channel program (Wed May 17 14:58:30 2017)
  • waiting for system load (4.49) to calm down, total wait time: 2 hr 18 min (Wed May 17 14:58:30 2017)
  • waiting for system load (3.38) to calm down, total wait time: 2 hr 18 min (Wed May 17 14:59:12 2017)
  • waiting for system load (3.01) to calm down, total wait time: 2 hr 18 min (Wed May 17 14:59:26 2017)
  • running now (Wed May 17 14:59:34 2017)
  • created 2 channel files (Wed May 17 15:00:35 2017)
  • Download MRC files: 1 2 (Wed May 17 15:00:35 2017)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 17 15:00:35 2017)
  • UCSF Chimera created Jmol compatible file (Wed May 17 15:00:40 2017)
  • compressing channel-001.obj (Wed May 17 15:00:40 2017)
  • waiting for system load (6.31) to calm down, total wait time: 2 hr 21 min (Wed May 17 15:00:40 2017)
  • waiting for system load (4.27) to calm down, total wait time: 2 hr 21 min (Wed May 17 15:03:10 2017)
  • waiting for system load (4.75) to calm down, total wait time: 2 hr 22 min (Wed May 17 15:03:45 2017)
  • waiting for system load (5.00) to calm down, total wait time: 2 hr 23 min (Wed May 17 15:04:38 2017)
  • waiting for system load (5.05) to calm down, total wait time: 2 hr 25 min (Wed May 17 15:05:42 2017)
  • running now (Wed May 17 15:06:49 2017)
  • waiting for system load (3.75) to calm down, total wait time: 2 hr 25 min (Wed May 17 15:06:49 2017)
  • waiting for system load (3.82) to calm down, total wait time: 2 hr 25 min (Wed May 17 15:07:10 2017)
  • waiting for system load (3.88) to calm down, total wait time: 2 hr 26 min (Wed May 17 15:07:33 2017)
  • waiting for system load (3.92) to calm down, total wait time: 2 hr 26 min (Wed May 17 15:07:57 2017)
  • waiting for system load (4.06) to calm down, total wait time: 2 hr 27 min (Wed May 17 15:08:22 2017)
  • running now (Wed May 17 15:08:50 2017)
  • UCSF Chimera completed in 8 min 15 sec (Wed May 17 15:08:51 2017)
  • analyzing volume (Wed May 17 15:08:51 2017)
  • normal CoM (-37.7, -37.0, -37.5) Å (Wed May 17 15:08:51 2017)
  • reduced center failed (Wed May 17 15:08:51 2017)
  • volume analysis completed in 21.22 msec (Wed May 17 15:08:51 2017)
  • compressing channel-001.mrc (Wed May 17 15:08:51 2017)
  • waiting for system load (4.31) to calm down, total wait time: 2 hr 27 min (Wed May 17 15:08:51 2017)
  • waiting for system load (4.16) to calm down, total wait time: 2 hr 28 min (Wed May 17 15:09:27 2017)
  • waiting for system load (4.10) to calm down, total wait time: 2 hr 28 min (Wed May 17 15:09:59 2017)
  • waiting for system load (4.06) to calm down, total wait time: 2 hr 29 min (Wed May 17 15:10:29 2017)
  • waiting for system load (4.04) to calm down, total wait time: 2 hr 29 min (Wed May 17 15:10:57 2017)
  • running now (Wed May 17 15:11:26 2017)
  • waiting for system load (3.87) to calm down, total wait time: 2 hr 30 min (Wed May 17 15:11:26 2017)
  • waiting for system load (3.29) to calm down, total wait time: 2 hr 30 min (Wed May 17 15:11:49 2017)
  • running now (Wed May 17 15:12:02 2017)
  • imaging volume (download mrc) with UCSF Chimera (Wed May 17 15:12:02 2017)
  • UCSF Chimera created Jmol compatible file (Wed May 17 15:12:06 2017)
  • compressing channel-002.obj (Wed May 17 15:12:06 2017)
  • waiting for system load (2.87) to calm down, total wait time: 2 hr 30 min (Wed May 17 15:12:06 2017)
  • waiting for system load (3.20) to calm down, total wait time: 2 hr 30 min (Wed May 17 15:12:13 2017)
  • waiting for system load (3.94) to calm down, total wait time: 2 hr 30 min (Wed May 17 15:12:23 2017)
  • waiting for system load (5.45) to calm down, total wait time: 2 hr 32 min (Wed May 17 15:12:49 2017)
  • waiting for system load (7.08) to calm down, total wait time: 2 hr 36 min (Wed May 17 15:14:17 2017)
  • waiting for system load (7.79) to calm down, total wait time: 2 hr 41 min (Wed May 17 15:18:02 2017)
  • waiting for system load (6.27) to calm down, total wait time: 2 hr 43 min (Wed May 17 15:23:15 2017)
  • waiting for system load (5.96) to calm down, total wait time: 2 hr 45 min (Wed May 17 15:25:42 2017)
  • running now (Wed May 17 15:27:44 2017)
  • waiting for system load (5.89) to calm down, total wait time: 2 hr 47 min (Wed May 17 15:27:44 2017)
  • waiting for system load (5.94) to calm down, total wait time: 2 hr 49 min (Wed May 17 15:29:41 2017)
  • waiting for system load (5.63) to calm down, total wait time: 2 hr 51 min (Wed May 17 15:31:42 2017)
  • waiting for system load (5.91) to calm down, total wait time: 2 hr 53 min (Wed May 17 15:33:22 2017)
  • waiting for system load (6.19) to calm down, total wait time: 2 hr 55 min (Wed May 17 15:35:20 2017)
  • waiting for system load (6.17) to calm down, total wait time: 2 hr 58 min (Wed May 17 15:37:40 2017)
  • waiting for system load (5.75) to calm down, total wait time: 2 hr 59 min (Wed May 17 15:39:59 2017)
  • waiting for system load (6.23) to calm down, total wait time: 3 hr 2 min (Wed May 17 15:41:46 2017)
  • waiting for system load (6.17) to calm down, total wait time: 3 hr 4 min (Wed May 17 15:44:09 2017)
  • running now (Wed May 17 15:46:28 2017)
  • UCSF Chimera completed in 34 min 26 sec (Wed May 17 15:46:28 2017)
  • analyzing volume (Wed May 17 15:46:28 2017)
  • normal CoM (-34.2, -37.2, -33.4) Å (Wed May 17 15:46:28 2017)
  • reduced center failed (Wed May 17 15:46:28 2017)
  • volume analysis completed in 30.78 msec (Wed May 17 15:46:28 2017)
  • compressing channel-002.mrc (Wed May 17 15:46:28 2017)
  • waiting for system load (6.14) to calm down, total wait time: 3 hr 6 min (Wed May 17 15:46:28 2017)
  • waiting for system load (6.37) to calm down, total wait time: 3 hr 9 min (Wed May 17 15:48:44 2017)
  • waiting for system load (6.97) to calm down, total wait time: 3 hr 12 min (Wed May 17 15:51:19 2017)
  • waiting for system load (7.42) to calm down, total wait time: 3 hr 17 min (Wed May 17 15:54:52 2017)
  • waiting for system load (7.57) to calm down, total wait time: 3 hr 22 min (Wed May 17 15:59:17 2017)
  • waiting for system load (7.92) to calm down, total wait time: 3 hr 27 min (Wed May 17 16:04:01 2017)
  • waiting for system load (8.33) to calm down, total wait time: 3 hr 34 min (Wed May 17 16:09:32 2017)
  • waiting for system load (8.13) to calm down, total wait time: 3 hr 40 min (Wed May 17 16:16:06 2017)
  • waiting for system load (6.97) to calm down, total wait time: 3 hr 43 min (Wed May 17 16:22:09 2017)
  • waiting for system load (7.81) to calm down, total wait time: 3 hr 49 min (Wed May 17 16:25:42 2017)
  • waiting for system load (7.72) to calm down, total wait time: 3 hr 54 min (Wed May 17 16:30:58 2017)
  • waiting for system load (7.51) to calm down, total wait time: 3 hr 58 min (Wed May 17 16:36:01 2017)
  • running now (Wed May 17 16:40:38 2017)
  • waiting for system load (7.75) to calm down, total wait time: 4 hr 3 min (Wed May 17 16:40:38 2017)
  • waiting for system load (7.71) to calm down, total wait time: 4 hr 8 min (Wed May 17 16:45:45 2017)
  • waiting for system load (7.64) to calm down, total wait time: 4 hr 13 min (Wed May 17 16:50:48 2017)
  • waiting for system load (7.43) to calm down, total wait time: 4 hr 18 min (Wed May 17 16:55:41 2017)
  • waiting for system load (7.55) to calm down, total wait time: 4 hr 22 min (Wed May 17 17:00:07 2017)
  • waiting for system load (7.67) to calm down, total wait time: 4 hr 27 min (Wed May 17 17:04:48 2017)
  • waiting for system load (7.37) to calm down, total wait time: 4 hr 32 min (Wed May 17 17:09:45 2017)
  • waiting for system load (7.69) to calm down, total wait time: 4 hr 37 min (Wed May 17 17:14:04 2017)
  • waiting for system load (6.82) to calm down, total wait time: 4 hr 40 min (Wed May 17 17:19:03 2017)
  • waiting for system load (7.66) to calm down, total wait time: 4 hr 45 min (Wed May 17 17:22:20 2017)
  • waiting for system load (7.44) to calm down, total wait time: 4 hr 49 min (Wed May 17 17:27:16 2017)
  • running now (Wed May 17 17:31:43 2017)
  • tarring file list (Wed May 17 17:31:44 2017)
  • waiting for system load (7.36) to calm down, total wait time: 4 hr 54 min (Wed May 17 17:31:44 2017)
  • waiting for system load (7.75) to calm down, total wait time: 4 hr 59 min (Wed May 17 17:36:01 2017)
  • waiting for system load (7.28) to calm down, total wait time: 5 hr 3 min (Wed May 17 17:41:09 2017)
  • waiting for system load (7.40) to calm down, total wait time: 5 hr 7 min (Wed May 17 17:45:17 2017)
  • waiting for system load (7.62) to calm down, total wait time: 5 hr 12 min (Wed May 17 17:49:39 2017)
  • waiting for system load (7.78) to calm down, total wait time: 5 hr 17 min (Wed May 17 17:54:30 2017)
  • waiting for system load (7.19) to calm down, total wait time: 5 hr 21 min (Wed May 17 17:59:42 2017)
  • waiting for system load (7.06) to calm down, total wait time: 5 hr 25 min (Wed May 17 18:03:39 2017)
  • waiting for system load (8.00) to calm down, total wait time: 5 hr 31 min (Wed May 17 18:07:22 2017)
  • waiting for system load (7.19) to calm down, total wait time: 5 hr 35 min (Wed May 17 18:13:05 2017)
  • waiting for system load (7.65) to calm down, total wait time: 5 hr 39 min (Wed May 17 18:17:02 2017)
  • running now (Wed May 17 18:21:57 2017)
  • waiting for system load (7.50) to calm down, total wait time: 5 hr 44 min (Wed May 17 18:21:57 2017)
  • waiting for system load (7.42) to calm down, total wait time: 5 hr 48 min (Wed May 17 18:26:31 2017)
  • waiting for system load (7.88) to calm down, total wait time: 5 hr 54 min (Wed May 17 18:30:56 2017)
  • waiting for system load (7.68) to calm down, total wait time: 5 hr 59 min (Wed May 17 18:36:22 2017)
  • waiting for system load (7.64) to calm down, total wait time: 6 hr 4 min (Wed May 17 18:41:20 2017)
  • waiting for system load (7.90) to calm down, total wait time: 6 hr 9 min (Wed May 17 18:46:13 2017)
  • waiting for system load (7.79) to calm down, total wait time: 6 hr 14 min (Wed May 17 18:51:42 2017)
  • waiting for system load (7.75) to calm down, total wait time: 6 hr 20 min (Wed May 17 18:56:55 2017)
  • waiting for system load (7.79) to calm down, total wait time: 6 hr 25 min (Wed May 17 19:02:03 2017)
  • waiting for system load (7.82) to calm down, total wait time: 6 hr 30 min (Wed May 17 19:07:16 2017)
  • waiting for system load (8.13) to calm down, total wait time: 6 hr 36 min (Wed May 17 19:12:34 2017)
  • waiting for system load (8.51) to calm down, total wait time: 6 hr 43 min (Wed May 17 19:18:36 2017)
  • running now (Wed May 17 19:25:40 2017)
  • compressing channel-001.mrc (Wed May 17 19:25:41 2017)
  • waiting for system load (7.66) to calm down, total wait time: 6 hr 48 min (Wed May 17 19:25:41 2017)
  • waiting for system load (7.17) to calm down, total wait time: 6 hr 52 min (Wed May 17 19:30:36 2017)
  • waiting for system load (6.69) to calm down, total wait time: 6 hr 55 min (Wed May 17 19:34:31 2017)
  • waiting for system load (6.44) to calm down, total wait time: 6 hr 58 min (Wed May 17 19:37:36 2017)
  • waiting for system load (6.42) to calm down, total wait time: 7 hr 0 min (Wed May 17 19:40:17 2017)
  • waiting for system load (6.30) to calm down, total wait time: 7 hr 3 min (Wed May 17 19:42:56 2017)
  • waiting for system load (6.00) to calm down, total wait time: 7 hr 5 min (Wed May 17 19:45:25 2017)
  • waiting for system load (5.99) to calm down, total wait time: 7 hr 7 min (Wed May 17 19:47:31 2017)
  • waiting for system load (6.04) to calm down, total wait time: 7 hr 9 min (Wed May 17 19:49:35 2017)
  • running now (Wed May 17 19:51:43 2017)

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Log file display

Show last lines of log file 
Terminal display
		
Message: waiting for system load (6.69) to calm down, total wait time: 6 hr 55 min 
Message: waiting for system load (6.44) to calm down, total wait time: 6 hr 58 min 
Message: waiting for system load (6.42) to calm down, total wait time: 7 hr min 
Message: waiting for system load (6.30) to calm down, total wait time: 7 hr 3 min 
Message: waiting for system load (6.00) to calm down, total wait time: 7 hr 5 min 
Message: waiting for system load (5.99) to calm down, total wait time: 7 hr 7 min 
Message: waiting for system load (6.04) to calm down, total wait time: 7 hr 9 min 
Message: running now 
Traceback (most recent call last): 
File "/var/www/html/3vee/py/runChannelFinder.py", line 67, in  
runthreev.start() 
File "/var/www/html/3vee/py/runChannelFinder.py", line 57, in start 
self.threev.webMrcSection(mrcfiles, self.website, f, pdb=True, pymol=self.params['pymol']) 
File "/var/www/html/py/ThreeVLib.py", line 1033, in webMrcSection 
gzmrcfile = self.gzipFile(mrcfile, pymol) 
File "/var/www/html/py/ThreeVLib.py", line 853, in gzipFile 
header = mrc.readHeaderFromFile(fname) 
File "/var/www/html/py/pyami/mrc.py", line 666, in readHeaderFromFile 
f = open(filename) 
IOError: [Errno 2] No such file or directory: '/var/www/html/3vee/output/2017/may17/b6c/channel-001.mrc' 

		


Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
Download source code
Help
Site news and updates
If you find this useful or want more functionality please contact Neil <vossman77 [at] yahoo.com>
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