Error 137

[shadowind]

Hi I'm facing an error 137 while trying to do assembly, couldnt find too much information, would appreciate any help

The error I recieved:

bash: line 1:  6785 Killed                  abyss-stack-size 65536 abyss-bloom-dbg -k96 -q3 --kc=3 -v -b1G -H4 -j30 sr/20071D-13-01_S45_L002_R1_001.fastq.g
z sr/20071D-13-01_S45_L002_R2_001.fastq.gz sr/20071D-13-02_S46_L002_R1_001.fastq.gz sr/20071D-13-02_S46_L002_R2_001.fastq.gz > ec_Wa_pr1.abyss2-1.fa
make[1]: *** [ec_Wa_pr1.abyss2-1.fa] Error 137

More log and error file: https://drive.google.com/file/d/1MUWrle3l4_nyhURF4wzdVtNpCJnxg5pi/view?usp=sharing

The command I ran:

export WG=$HOME/wengen/wengan-v0.2-bin-Linux/wengan.pl
export LR=$HOME/fastq/lr
export SR=$HOME/fastq/sr

perl ${WG} -x pacraw -a A -s ${SR}/20071D-13-01_S45_L002_R1_001.fastq.gz,${SR}/20071D-13-01_S45_L002_R2_001.fastq.gz,${SR}/20071D-13-02_S46_L002_R1_001.fastq.gz,${SR}/20071D-13-02_S46_L002_R2_001.fastq.gz -l ${LR}/m64284e_220320_125421.fastq.gz,${LR}/m64284e_220321_190548.fastq.gz,${LR}/m64284e_220326_230326.fastq.gz,${LR}/m64284e_220328_051513.fastq.gz -p ec_Wa_pr1 -t 20 -g 5

[adigenova]

Hi, It seems that your job was killed,, are you using a cluster to run the jobs?

Best Alex

[shadowind]

thank you for the quick response. I'm using single m5.8xlarge aws instance, 128GB/32CPU. seems OOM. Is wengan support running distributed on cluster?

[adigenova]

Wengan can run in a single node of a cluster, we do not support MPI. It seems that the genome that you are assembly is very large, at least when looking at the Abyss log

Assembled 49839000000 bp in 519156251 contigs
Assembled 49840000512 bp in 519166673 contigs
Assembled 49841017248 bp in 519177264 contigs

What is the size of the genome? I think that the problem was the running time, then it was killed by the scheduler. Best Alex

[shadowind]

Could be the long read and short reads are 130GB each seperate into 4 files