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IDProjectCategoryView StatusDate SubmittedLast Update
0002516graphvizDotpublic2015-02-09 11:152015-02-09 14:31
Reporterchefarov 
Assigned To 
PrioritynormalSeveritycriticalReproducibilityhave not tried
StatusnewResolutionopen 
PlatformUbuntu x86_64OSLinux OS Version 3.13.0-45-gener
Summary0002516: dot killed
DescriptionSSPACE scaffolder came up with 3 .dot files (prefix_part1.dot, prefix_part2.dot, prefix_part3.dot).

I tried to use both only the part1.dot (final output), and the concatenated result from three files:

dot -Tps2 prefix.visual_scaffolds.part1.dot -v ? -o pic.ps &> dot.log
dot -Tps2 all.dot -v ? -o pic.ps &> all_dot.log

coming up to the same problem that the script is killed without a meaningfull output:


dot.log (head + tail):

dot - graphviz version 2.36.0 (20140111.2315)
libdir = "/usr/lib/graphviz"
Activated plugin library: libgvplugin_core.so.6
Using render: ps:core
Using device: ps2:ps:core
Activated plugin library: libgvplugin_dot_layout.so.6
Using layout: dot:dot_layout
The plugin configuration file:
    /usr/lib/graphviz/config6
        was successfully loaded.
    render : cairo dot fig gd map pic pov ps svg tk vml vrml xdot
    layout : circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi
    textlayout : textlayout
    device : canon cmap cmapx cmapx_np dot eps fig gd gd2 gif gv imap imap_np ismap jpe jpeg jpg pdf pic plain plain-ext png pov ps ps2 svg svgz tk vml vmlz vrml wbmp x11 xdot xdot1.2 xdot1.4 xlib
    loadimage : (lib) eps gd gd2 gif jpe jpeg jpg png ps svg xbm
fontname: "Times-Roman" resolved to: (ps:pango Nimbus Roman No9 L, REGULAR) (PangoCairoFcFont) "Nimbus Roman No9 L, Regular" /usr/share/fonts/type1/gsfonts/n021003l.pfb
network simplex: 4 nodes 3 edges maxiter=2147483647 balance=1
network simplex: 4 nodes 3 edges 0 iter 0.00 sec
network simplex: 5 nodes 4 edges maxiter=2147483647 balance=1
network simplex: 5 nodes 4 edges 0 iter 0.00 sec

.........

mincross: pass 2 iter 0 trying 0 cur_cross 0 best_cross 0
mincross: pass 2 iter 0 trying 0 cur_cross 0 best_cross 0
mincross: pass 2 iter 0 trying 0 cur_cross 0 best_cross 0
mincross ROOT: 0 crossings, 403.78 secs.

(thousands of mincross: 2 0 0 0 0 values repeating in the middle).

The all_dot.log file is similar. It's attached below
Steps To ReproduceDescribed above
Additional Informationgraphviz 2.36.0-0ubuntu3.1 amd64
TagsNo tags attached.
AUXILLARY-FILES
DATE-FIXED
FIX-COMMENT
FORMER-ID
INPUT-FILE
OUTPUT-FILE
STATUS-COMMENT
VERSION2.36.0 (20140111.2315)
Attached Files

- Relationships

-  Notes
User avatar (0000874)
chefarov (reporter)
2015-02-09 11:19

Log file: http://cineserver.3p.tuc.gr/d/all_dot.log [^]
User avatar (0000875)
north (administrator)
2015-02-09 11:20

Please can you attach one of the files you are trying to render, such as prefix_part1.dot? Thank you.
User avatar (0000876)
chefarov (reporter)
2015-02-09 14:31

of course. I should have done it before.
http://cineserver.3p.tuc.gr/hosted/dna/SRR065390_scaffolds.visual_scaffolds.part1.dot [^]

- Issue History
Date Modified Username Field Change
2015-02-09 11:15 chefarov New Issue
2015-02-09 11:19 chefarov Note Added: 0000874
2015-02-09 11:20 north Note Added: 0000875
2015-02-09 14:31 chefarov Note Added: 0000876


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