brianjohnhaas
commented
4 years ago Hi,
I'm not sure what remora is, but I suspect the issue lies there.
On Tue, Mar 17, 2020 at 5:16 PM kbeavers notifications@github.com wrote:
After 48 hours my jobs keep timing out with no obvious error messages and no output files created. Here is my script that I use on the TACC Lonestar 5 server:
!/bin/bash
SBATCH -J pporthread4
SBATCH -o pporthread4.o%j
SBATCH -e pporthread4.e%j
SBATCH -N 2
SBATCH -n 32
SBATCH -p largemem512GB
SBATCH -t 48:00:00
Other commands must follow all #SBATCH directives...
module load intel/18.0.2 module load remora/1.8.2 module load TACC-largemem module load bowtie/2.3.4 module load trinityrnaseq/2.8.4 run the executable named a.out
remora Trinity --normalize_reads --seqType fq --grid_node_CPU 32 --grid_node_max_memory 500G --max_memory 500G --SS_lib_type FR --left UVI_120_F_paired.fq.gz,UVI_122_F_paired.fq.gz,UVI_124_F_paired.fq.gz --right UVI_120_R_paired.fq.gz,UVI_122_R_paired.fq.gz,UVI_124_R_paired.fq.gz --CPU 32
The only error I get is: "Host key verification failed."
I have no idea what's going on here. Can someone lead me in the right direction?
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/BerlinTrinityWorkshop2018/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX6KTJWQBZN4YCTFW73RH7SBPANCNFSM4LN3QWYA .
--
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
After 48 hours my jobs keep timing out with no obvious error messages and no output files created. Here is my script that I use on the TACC Lonestar 5 server:
!/bin/bash
SBATCH -J pporthread4
SBATCH -o pporthread4.o%j
SBATCH -e pporthread4.e%j
SBATCH -N 2
SBATCH -n 32
SBATCH -p largemem512GB
SBATCH -t 48:00:00
Other commands must follow all #SBATCH directives...
module load intel/18.0.2 module load remora/1.8.2 module load TACC-largemem module load bowtie/2.3.4 module load trinityrnaseq/2.8.4
run the executable named a.out
remora Trinity --normalize_reads --seqType fq --grid_node_CPU 32 --grid_node_max_memory 500G --max_memory 500G --SS_lib_type FR --left UVI_120_F_paired.fq.gz,UVI_122_F_paired.fq.gz,UVI_124_F_paired.fq.gz --right UVI_120_R_paired.fq.gz,UVI_122_R_paired.fq.gz,UVI_124_R_paired.fq.gz --CPU 32
The only error I get is: "Host key verification failed."
I have no idea what's going on here. Can someone lead me in the right direction?