Problem Running Trinity TransDecoder

Question

[pld]

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

/apps/trinity/trinityrnaseq_r20131110/trinity-plugins/transdecoder/TransDecoder line

467.

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.

Answer 1

[Chris Fields]

A perl exit code of 256 is the value from the wait call and should be shifted right by eight (C apparently does the same). So, an exit code of 256 corresponds to an exit code of 1, which means a general error. This could mean anything from errors in the code to permissions issues.

Try capturing the exit code in bash right after you run CD-HIT; it's possible it exits with a code you don't catch when running in the shell.

cd-hit-est .....
echo $?