Looks like the 24 hours of redoing the libc++ is working out.

CMD finished (161 seconds)

Thursday, August 14, 2014: 21:56:02     CMD: touch /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_004_Arjam_MOE/output_4/chrysalis/file_partitioning.ok

CMD finished (0 seconds)

---------------------------------------------------

----------- Chrysalis: QuantifyGraph --------------

-- (Integrate mapped reads into de Bruijn graph) --

---------------------------------------------------

Thursday, August 14, 2014: 21:56:03     CMD: /usr/local/Cellar/trinity/r20131110/trinity-plugins/parafly/bin/ParaFly -c /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_004_Arjam_MOE/output_4/chrysalis/quantifyGraph_commands -CPU 4 -failed_cmds failed_quantify_graph_commands.82191.txt -v -shuffle

Number of  Commands: 57201

succeeded(48273)   84.3919% completed.

...several hours later...

Butterfly finished too!
72,120 transcripts were assembled. Are there any ORs? Gah, I hope so... :-|