I am attempting to run TransDecoder on transcriptome data generated by trinity. I have installed CD-HIT and exported the path correctly but TransDecoder fails when trying to run cd-hit-est.
Error, cmd: /data/xxx/src/cd-hit/cd-hit-v4.5.4-2011-03-07/cd-hit-est -r 1 -i /spin1
/users/xxx/trinity-transdecoder/redundant_top -o /spin1/users/xxx/trinity-transdecoder
/redundant_top.nr90 -M 0 -T 20 >/dev/null 2>/dev/null died with ret 256 at /usr/local
However if I copy and paste this command and try and run it, it seems that cd-hit-est runs correctly and exits without error. I'm not sure what is wrong, if TransDecoder was unable to find the cd-hit-ext executable, it would crash before getting to this point, but it does not.