48hour Timeout with zero files created, no obvious errors

[ghost]

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?

[brianjohnhaas]

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 ***@***.***> 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 <#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>