Process killed in Line 177 of CLARKSCV1.2.6.1/classify_metagenome.sh

[Melissa Gray]

A couple weeks ago, I was able to use set_target.sh and classify_metagenome.sh for the default Bacteria databases as well as some custom databases. Yesterday, for a custom database (one with only Bacteria metagenomes from 2019 and before), I ran into a segmentation fault error.

I ran the script again, this time with 1000G (1T) of memory just in case. The segmentation fault was gone, but I got a different error:

-> ifs/groups/rosenGrp/mag535/CLARKSCV1.2.6.1/classify_metagenome.sh: line 177: 35477 Killed                  $LDIR/exe/CLARK $PARAMS

The full job output:

-> CLARK version 1.2.6.1 (UCR CS&E. Copyright 2013-2019 Rachid Ounit, roun...@cs.ucr.edu)

-> The program did not find the database files for the provided settings and reference sequences (4520 targets). The program will build them.

-> Starting the creation of the database of targets specific 31-mers from input files...

->  Progress report: (6989/15406)    /ifs/groups/rosenGrp/mag535/CLARKSCV1.2.6.1/classify_metagenome.sh: line 177: 35477 Killed                  $LDIR/exe/CLARK $PARAMS

-> The database is /beegfs/scratch/mag535/CLARK/2019_clark_db

-> The sample is /beegfs/scratch/mag535/ZZ_real_sample.fa

-> Classification time is 48060

This is the line in my job script (the paths were simplified):

-> CLARKSCV1.2.6.1/classify_metagenome.sh -O ZZ_real_sample.fa -R clark_2019_real_sample -n 24

My job script ran to completion, but the process for building the 31-mer hash table was killed about halfway through and it gave a '/ifs/groups/rosenGrp/mag535/CLARKSCV1.2.6.1/classify_metagenome.sh: line 177: 35477 Killed                  $LDIR/exe/CLARK $PARAMS' error this time.

I checked the classify_metagenome.sh script in CLARKSCV1.2.6.1, and this is line 177, where the process got killed:

-> $LDIR/exe/CLARK $PARAMS

I can't figure out why that process is getting killed, can you help me?

[Rachid]

Hello mgsj...,

I am sorry to hear your program was killed. 

Please contact your helpdesk for your information, maybe the program memory usage (virtual or real) exceeded some limit set by your IT team?

Best,

Rachid