Getting error code -9 on digital ocean droplet

[tayabsoomro]

Hi, I am trying to run Megahit on digital ocean droplet and I am getting the following error:

/mnt/genomagic_volume/mhit_output/tmp/k27/27 --num_cpu_threads 2 -k 27 --kmer_from 0 --input_prefix /mnt/genomagic_volume/mhit_output/tmp/k27/27 --need_mercy; Exit code -9

I have tried it without --k-min argument, with 27 and 31 as --k-min values but I am still getting the same issue.

Here is the full log:

root@genomagic:/mnt/genomagic_volume# megahit -r bsub3557_minion.fastq -o mhit_output -m 0.5 --k-min 27
2020-05-03 08:12:03 - MEGAHIT v1.2.9
2020-05-03 08:12:03 - Using megahit_core with POPCNT and BMI2 support
2020-05-03 08:12:03 - Convert reads to binary library
2020-05-03 08:12:30 - INFO  sequence/io/sequence_lib.cpp  :   77 - Lib 0 (/mnt/genomagic_volume/bsub3557_minion.fastq): se, 293528 reads, 75213 max length
2020-05-03 08:12:30 - INFO  utils/utils.h                 :  152 - Real: 27.1427        user: 10.5561   sys: 2.5502     maxrss: 232016
2020-05-03 08:12:30 - Start assembly. Number of CPU threads 2
2020-05-03 08:12:30 - k list: 27,37,47,57,67,77,87,97,107,117,127,137,141
2020-05-03 08:12:30 - Memory used: 2068283392
2020-05-03 08:12:30 - Extract solid (k+1)-mers for k = 27
2020-05-03 08:19:29 - Build graph for k = 27
2020-05-03 08:27:02 - Error occurs, please refer to /mnt/genomagic_volume/mhit_output/log for detail
2020-05-03 08:27:02 - Command: /root/MEGAHIT-1.2.9-Linux-x86_64-static/bin/megahit_core seq2sdbg --host_mem 2068283392.0 --mem_flag 1 --output_prefix /mnt/genomagic_volume/mhit_output/tmp/k27/27 --num_cpu_threads 2 -k 27 --kmer_from 0 --input_prefix /mnt/genomagic_volume/mhit_output/tmp/k27/27 --need_mercy; Exit code -9

Any suggestions?

[tayabsoomro]

Anything?

[fconstancias]

same here... I am trying to assemble huge dataset, I guess that's why...

[voutcn]

-9 means that the program was killed by SIGKILL. If you are using a server that is managed by another system (e.g. an admin is managing the server by some cluster management system, or this program/container was run by docker/k8s with CPU/memory limits), the program will be killed if it exceeds the memory limit.

It is also possible that you share the server with other users, and other users (with root permission) can manually send SIGKILL to kill your process.