[sharp-discuss] - peak list from residual map
Clemens Vonrhein
vonrhein@globalphasing.com
Tue, 12 Mar 2002 16:54:50 +0000
Dear venkataraman,
according to your log file (which is $BDG_home/sushi/logs/error_log
btw) it seems that the file down't exist:
> Unable to determine CCP4 version from file /tmp/6961.dir/peaks.log
> (No such file or directory)
I'm not quite sure why this could happen. But some hints:
- can you actually view this residual map (using e.g. O)?
- what Perl version are you running (see BDG_perl variable in
$BDG_home/machines/*/host.setup)? See notes in the installation
manual ..
- have you changed the RMS limits for the peak picking? The defaults
usually work fine ...
- just after it crashes: is the /tmp/XXXX.dir still there? What's in
it? What does the peaks.log file (if present) contain?
You can always run the checkBDG.sh script (from
http://www.globalphasing.com/sharp/installation/index.html#trouble).
Hope that helps.
Cheers
Clemens
PS: it runs without problems on our various RedHat 7.x machines - so I
don't think it is related to that.
On Tue, Mar 12, 2002 at 10:25:07AM -0500, Venkataraman Kabaleeswaran wrote:
> I got the following error messages when I tried to pick peaks on a residual
> map in autosharp. (sharp 3.0.2 & ccp4 4.1.1 in redhat 7.2). The peak.log
> file was created in the tmp directory by CCP4, but it didnot display on the
> Sharp windows, this worked properly in sharp (2.0).
>
> any suggestions
>
> thanks
> venkataraman
>
>
> --------------------
>
>
> !DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN//2.0"><html>
> <head>
> <title>Peak list</title>
> </head>
> <body bgcolor="#FFFAFO" text="#00000O" alink="#FF0000" link="#0000C0" >
> <CENTER><H1>Peak list</H1><H3>Compound 1 - Crystal 1 - Wavelength 1 - Batch 1
> - ANO</H3></CENTER>
> <center><H3>User: <font color="#AA2244">vk</font> Project
> ID: <font color="#AA2244">new-mad.5</font></H3></center>
> <HR NOSHADE>
> Checking peaks against <A
> HREF="/users/vk/cardfiles/end_new-mad.5.sin">cardfiles/end_new-mad.5.sin</a><BR><P>
> <PRE>
> </FONT></PRE></TABLE></TABLE></UL></UL></OL></OL>
> <P><HR NOSHADE><P><B>ERROR in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl</B>
> <FONT COLOR="#CC00EE"><P>Undefined error: The following return values are set:
> <UL>
> <LI>Child error = 2
> <LI>OS error = No such file or directory
> <LI>Eval error =
> </UL>
> </FONT>
> <P><HR NOSHADE><P>
> <P>Last entries in the http daemon log file:<P>
> <PRE>
> [Fri Jan 25 11:13:47 2002] [notice] Apache/1.3.22 (Unix) configured --
> resuming normal operations
> [Fri Jan 25 11:13:47 2002] [notice] Accept mutex: sysvsem (Default: sysvsem)
> [Fri Feb 1 14:48:57 2002] [notice] Apache/1.3.22 (Unix) configured --
> resuming normal operations
> [Fri Feb 1 14:48:57 2002] [notice] Accept mutex: sysvsem (Default: sysvsem)
> Unable to determine CCP4 version from file /tmp/4672.dir/peaks.log
> (No such file or directory)
> Undefined error in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl
> Unable to determine CCP4 version from file /tmp/32495.dir/peaks.log
> (No such file or directory)
> Undefined error in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl
> [Tue Feb 26 18:36:27 2002] [notice] caught SIGTERM, shutting down
> [Tue Feb 26 18:44:41 2002] [notice] Apache/1.3.22 (Unix) configured --
> resuming normal operations
> [Tue Feb 26 18:44:41 2002] [notice] Accept mutex: sysvsem (Default: sysvsem)
> rm: cannot remove `new-mad.6': No such file or directory
> mkdir: cannot create directory `new-mad.6': File exists
> Unable to determine CCP4 version from file /tmp/4334.dir/peaks.log
> (No such file or directory)
> Undefined error in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl
> Unable to determine CCP4 version from file /tmp/5307.dir/peaks.log
> (No such file or directory)
> Undefined error in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl
> Unable to determine CCP4 version from file /tmp/5737.dir/peaks.log
> (No such file or directory)
> Undefined error in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl
> Unable to determine CCP4 version from file /tmp/6868.dir/peaks.log
> (No such file or directory)
> Undefined error in /usr/pgm/sharp3/sushi/cgi-bin/peak.pl
> Error in script /usr/pgm/sharp3/sushi/cgi-bin/map.pl - No map selected for
> display! at /usr/pgm/sharp3/lib/libhtml.pl line 1415.
> Unable to determine CCP4 version from file /tmp/6961.dir/peaks.log
> (No such file or directory)
> </PRE>
> <PRE>
>
>
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