Question: Running trinity in DIAG grid ---- bash: error importing function definition for `module'
0
gravatar for sckinta
4.7 years ago by
sckinta480
United States
sckinta480 wrote:

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_jobhttp://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 -b y /diag/software/trinity/Trinity.pl --seqType fq --JM 50G --left SG_R1.fastq --right SG_R2.fastq  --CPU 8 --trimmomatic --quality_trimming_params LLUMINACLIP: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!

rna-seq • 1.9k views
ADD COMMENTlink modified 4.6 years ago by zulfikar30 • written 4.7 years ago by sckinta480
0
gravatar for zulfikar
4.6 years ago by
zulfikar30
Germany
zulfikar30 wrote:

Hi,

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

ADD COMMENTlink written 4.6 years ago by zulfikar30
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