Fatal error: cannot open the display: NIL

asked 2017-12-06 01:01:08 -0500

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When I use pathway-tools on command line, the command is ./pathway-tools -patho param-dir. The tools run at first and can save an ocelot db, then report this error. Pruning out unneeded reactions, compounds, super-pathways, etc... Delete pathways with no reactions in this species Adjusting predecessor list of super-pathway PWY-5703 Deleted 1357 orphan reactions and 771 compounds Inferring spontaneous reactions. Imported 23 spontaneous reactions. Deleted 314 publication frames that are not cited in the PGDB

Inferred 50 base pathways.

 :::::  Ending Pathway Inference at 2017-11-30 10:29:49  :::::

Inferring spontaneous reactions. Imported 0 spontaneous reactions. Creating report pathway file /picb/bdp/microbial-project/pipeline/zhixiaoyang/newmetacycdata/ptools-local/pgdbs/user/xnv4cyc/1.0/repor ts/pathways-report.txt. Build done. PGDB contains 608 genes, 601 proteins, 50 base pathways, 515 reactions, 619 compounds [Saving KB XNV4BASE to V4-FASL file /picb/bdp/microbial-project/pipeline/zhixiaoyang/newmetacycdata/ptools-local/pgdbs/user/xnv4cyc/1. 0/kb/xnv4base.ocelot 0 frames ignored 13257 frames saved] [Saving KB PGDB-METADATA to V1-SEXPR file /picb/bdp/microbial-project/pipeline/zhixiaoyang/newmetacycdata/ptools-local/pgdbs/user/PGDB -METADATA.ocelot 0 frames ignored 4 frames saved] Starting Hole Filler for XNV4.

30-Nov-2017 10:29:52 Fatal error: cannot open the display: NIL

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