Trinity Insilico Normalization

Question

[sansan96]

Hello, I am trying to run trinity but on two samples but I am confused. I need help please. The process tells me this:

perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
         LANGUAGE = (unset),
         LC_ALL = (unset),
         LANG="C.UTF-8"
     are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
=>> PBS: job killed: walltime 230442 exceeded limit 230400

My script is:

My command:

#PBS -N agave_assembly
#PBS -N agave_assembly
#PBS -l nodes=1:ppn=8,mem=250gb,vmem=250gb
#PBS -o trinity_output_insi.log
#PBS -e trinity_error_insi.log
#PBS -q ensam
#PBS -V
cd /LUSTRE/usuario/epola/transcriptomas_agave_2023/ensamble_novo
module load trinity/2.8.5
module load samtools/1.13
module load jellyfish/2.2.10
module load bowtie2/2.3.5.1
module load  Salmon/0.11.3
Trinity --seqType fq \
    --left ../trimeados_agave/P148H_R1_001_P.fastq.gz \
    --right ../trimeados_agave/P148H_R2_001_P.fastq.gz \
    --max_memory 164G \
    --CPU 8 \
    --output trinity_results_insilico

Answer 1

[Ram]

Read the error message - you ran out of time.

Add a walltime directive for PBS and set it to something > 230400s (64h) hours:

#PBS -l walltime=96:00:00

Also, you have a duplicate job name line, remove it and add the walltime line there instead.

[sansan96]

Thanks for you answer.

[Ram]

Hi,

If my answer resolved your question, please mark it as accepted.