Running trinity in DIAG grid ---- bash: error importing function definition for `module'

Question

[sckinta]

Hi,

Did anyone run pre-installed trinity on DIAG? I got an error like this :

bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'

I did exactly what the wiki told me to do: http://wiki.diagcomputing.org/index.php/Submitting_a_grid_job, http://wiki.diagcomputing.org/index.php/Trinity

source /diag/software/sge-root/diag/common/settings.sh
export PATH=$PATH:/diag/software/bin

then run trinity with my data

qsub \
  -P diag \
  -pe \
  make 8 \
  -q highmem.q \
  -V \
  -by /diag/software/trinity/Trinity.pl \
  --seqType fq \
  --JM 50G \
  --left SG_R1.fastq \
  --right SG_R2.fastq \
  --CPU 8 \
  --trimmomatic \
  --quality_trimming_params ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:36 -\
  -output Trinity_Output

I submitted this job on my working directory in which two fastq files and TruSeq3-PE.fa exist.

Anyone can help? Thank you!

[zulk]

Hi,

Dear sckinta did you successfully installed trinity on diag. Can you give me your e-mail.