Hi,
I too had a similar error when trying to process very weak
data integrated to the edge of a detector.
The log showed lots of "0.0" and "-nan".
Sometimes the program went into an infinite loop and
tried to consume all the memory of the system.
Applying a reasonable high resolution cutoff by SFTOOLS
solved the problem.
Best regards,
Takanori Nakane
On 2014-06-20 10:49, <Stephen Carr> wrote:
> Thanks for the help, the old version of truncate did the trick.
> Interestingly running the old version of truncate in either of the
> data reduction pipelines (with aimless or scala) produced mtz files
> containing no F's but the stand alone version produced an mtz with all
> the f's prsent.
>
>
>
> cheers,
>
>
>
> Steve
>
>
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email [log in to unmask]
> tel 01235 567717
> ________________________________
> From: Parthasarathy Sampathkumar [[log in to unmask]]
> Sent: 19 June 2014 19:55
> To: ccp4bb
> Subject: Re: [ccp4bb] ctruncate error
>
> Yes.., I too had similar problem with Ctruncate, and used older
> truncate to overcome the issue.
>
> Best Wishes,
> Partha
>
>
> On Thu, Jun 19, 2014 at 2:38 PM, jie liu
> <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hi
>
> I also encountered the same problem after recent updates (not the most
> recent one, but a couple of updates back). Choosing to run
> old-truncate will get it around.
>
> Best wishes
>
> Jie
>
> ----- Original Message ----- From: "<Stephen Carr>"
> <[log in to unmask]<mailto:[log in to unmask]>>
> To: <[log in to unmask]<mailto:[log in to unmask]>>
> Sent: Thursday, June 19, 2014 1:11 PM
> Subject: [ccp4bb] ctruncate error
>
>
>
> Dear CCP4bb,
>
> I am experiencing an unusual error when running truncate. The program
> appears to be converting I's to F's, but then failing to output them
> in the resulting mtz file, see mtzdump output below:
>
> Col Sort Min Max Num % Mean Mean Resolution
> Type Column
> num order Missing complete abs. Low High
> label
>
> 1 ASC 0 26 0 100.00 12.6 12.6 79.95 3.00
> H H
> 2 NONE 0 15 0 100.00 4.3 4.3 79.95 3.00
> H K
> 3 NONE -42 42 0 100.00 0.7 16.0 79.95 3.00
> H L
> 4 NONE 0.0 19.0 0 100.00 9.56 9.56 79.95 3.00
> I FreeR_flag
> 5 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
> F F_delta16
> 6 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
> Q SIGF_delta16
> 7 BOTH 0.0 0.0 25 99.81 0.00 0.00 42.22 3.00
> D DANO_delta16
> 8 BOTH 0.0 0.0 11253 13.22 0.00 0.00 42.22 3.00
> Q SIGDANO_delta16
> 9 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
> G F_delta16(+)
> 10 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
> L SIGF_delta16(+)
> 11 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
> G F_delta16(-)
> 12 BOTH ? ? 12968 0.00 ? ? -999.00 0.00
> L SIGF_delta16(-)
> 13 BOTH 0 0 25 99.81 0.0 0.0 42.22 3.00
> Y ISYM_delta16
> 14 NONE -8.9 72479.2 25 99.81 198.34 198.44 42.22 3.00
> J IMEAN_delta16
> 15 NONE 0.6 3135.7 25 99.81 5.25 5.25 42.22 3.00
> Q SIGIMEAN_delta16
> 16 NONE -10.8 72479.2 25 99.81 198.18 198.37 42.22 3.00
> K I_delta16(+)
> 17 NONE 0.0 3135.7 25 99.81 6.79 6.79 42.22 3.00
> M SIGI_delta16(+)
> 18 NONE -9.5 72479.2 25 99.81 198.30 198.47 42.22 3.00
> K I_delta16(-)
> 19 NONE 0.0 3135.7 25 99.81 6.70 6.70 42.22 3.00
> M SIGI_delta16(-)
>
>
> No. of reflections used in FILE STATISTICS 12968
>
> The truncate log file shows no obvious errors apart from the
> cumulative intensity plot which indicates no reflections, all other
> diagnostic indicators for data quality seem to suggest everything is
> ok. I get the error with both ctruncate and truncate and also
> automatically as part of the scaling/merging pipelines. The data were
> processed with imosflm, scaled with aimless with neither flagging any
> errors with the data. I am running CCP4 6.4.0 on a linux box (Centos
> 6) and have installed the latest updates. Any suggestions as to what
> the fault might be and how to get around it would be greatly
> appreciated.
>
> best wishes,
>
> Steve
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email
> [log in to unmask]<mailto:[log in to unmask]>
> tel 01235 567717
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