Smrt portal gmap "no such file or directory" error - pb-dyim/SMRT-Analysis GitHub Wiki

There is a bug in SMRT Analysis 1.4.0 pertaining only to the RS_Transcriptome_Mapping protocol. The error occurs because the path to the GMAP scripts are hard-coded instead of relative to $SEYMOUR_HOME. If you see the following error in your smrtpipe.log file:

[ERROR] 2013-04-17 17:41:30,404 [pbpy.smrtpipe.engine.SmrtPipeTasks run 655] > Can't exec "/home/NANOFLUIDICS/build/workspace/secondary-1.4-centos56/_output/smrtanalysis-1.4.0/analysis/bin/gmap_home/bin/fa_coords": No such file or directory at /opt/smrtanalysis/analysis/bin/gmap_build line 116.

Please edit lines 6 and 16 of SEYMOUR_HOME/analysis/bin/gmap_home/bin/gmap_build to restore full functionality.

Line 6 should be:

$gmapdb = $ENV{"SEYMOUR_HOME"} . "/analysis/bin/gmap_home/share";

Line 16 should be:

$bindir = $ENV{"SEYMOUR_HOME"} . "/analysis/bin/gmap_home/bin";