[wgs-assembler-users] CA getting stuck at stage 7-0-CGW

[Ray C. <rc...@ag...>]

Dear All,

       I am executing CA from Masurca, it seems to get stuck at the stage
"7-0-CGW" for 12 days. When I checked cgw.out, the last line says:

* AddScaffoldInferredEdges   scaffolds = 0

     I tried killing and restarting, then it got stuck at the same stage:

====> Reading ~/CA/7-0-CGW/genome.ckp.3 at Tue Dec 22 13:23:07 2015
* ScaffoldGraph Memory Report:
*     numElements AllocatedElements AllocatedSize
VA        448 bytes; elements:          7 active;          7 allocated;
 64 bytes; 'Dists'
VA 6373749984 bytes; elements:   66393229 active;   66393229 allocated;
 96 bytes; 'CIFrags'
VA 3691841920 bytes; elements:   23074012 active;   23074012 allocated;
160 bytes; 'CIs    '
VA 2730912384 bytes; elements:   28447004 active;   28447004 allocated;
 96 bytes; 'CIEdges'
VA 3691841920 bytes; elements:   23074012 active;   23074012 allocated;
160 bytes; 'Contigs    '
VA 2730912384 bytes; elements:   28447004 active;   28447004 allocated;
 96 bytes; 'ConEdges'
VA          0 bytes; elements:          0 active;          0 allocated;
160 bytes; 'Scaffolds'
VA          0 bytes; elements:          0 active;          0 allocated;
 96 bytes; 'SEdges'
* TotalMemorySize = 19219259040
Beginning CHECKPOINT_AFTER_CLEANING_SCAFFOLDS
* AddScaffoldInferredEdges   scaffolds = 0

     Does the log look strange? Has anyone seen this before?

Thanks!
Ray Cui

Max-Planck-Institut für Biologie des Alterns / Max Planck Institute for
Biology of Ageing
Wissenschaftlicher MA / Postdoctoral researcher
Office: Joseph-Stelzmann 9b, D-50931 Köln / Cologne
Postal address: Postfach 41 06 23, D-50866 Köln / Cologne
Tel.:+49 (0)221 496
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rc...@ag...
www.age.mpg.de