Failed to run script, 137 in the assembly step

[anacatalan]

Dear Chuan,
I am running the assembly necat step and after some days of running the script I got the following error:

Fri Apr 22 16:23:29 2022] INFO: mapping 67550 --- 67600 (78674) (asm_pm/asm_p/dss/dsslegfs01/pr53da/pr53da-dss-0032/assemblies/necat/luita/luita_necat/scripts/tr_al_vol_4.sh: line 16: 52867 Killed                  /dss/dsshome1/lxc07/lu32gib/miniconda3/share/necat-0.0.1_update20200803-1/bin/oc2asmpm -n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400 -u 1 -t 32 /dss/dsslegfs01/pr53da/pr53da-dss-0032/assemblies/necat/luita/luita_necat/2-trim_bases/pac_in 4 /dss/dsslegfs01/pr53da/pr53da-dss-0032/assemblies/necat/luita/luita_necat/2-trim_bases/pac_in/pm_result_4
2022-04-22 16:27:27 [Warning] Failed to run script, 137, /dss/dsslegfs01/pr53da/pr53da-dss-0032/assemblies/necat/luita/luita_necat/scripts/tr_al_vol_4.sh
2022-04-22 16:27:27 [Error] Reached to maximum number of script errors


I'm attaching the whole run output:
[necatAssembly_luita_2022-04-11.out.gz](https://github.com/xiaochuanle/NECAT/files/8542000/necatAssembly_luita_2022-04-11.out.gz)

And this is my configuration file:

PROJECT=luita_necat
ONT_READ_LIST=/dss/dsslegfs01/pr53da/pr53da-dss-0032/rawdata/Nanopore/op_025/data/op_025_001/fastq_pass/read_list.txt
GENOME_SIZE=925000000
THREADS=32
MIN_READ_LENGTH=3000
PREP_OUTPUT_COVERAGE=40
OVLP_FAST_OPTIONS=-n 500 -z 20 -b 2000 -e 0.5 -j 0 -u 1 -a 1000
OVLP_SENSITIVE_OPTIONS=-n 500 -z 10 -e 0.5 -j 0 -u 1 -a 1000
CNS_FAST_OPTIONS=-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0
CNS_SENSITIVE_OPTIONS=-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0
TRIM_OVLP_OPTIONS=-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 1 -a 400
ASM_OVLP_OPTIONS=-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400
NUM_ITER=2
CNS_OUTPUT_COVERAGE=40
CLEANUP=1
USE_GRID=false
GRID_NODE=
GRID_OPTIONS=
SMALL_MEMORY=0
FSA_OL_FILTER_OPTIONS="-min_coverage 3"
FSA_ASSEMBLE_OPTIONS=""
FSA_CTG_BRIDGE_OPTIONS=""
POLISH_CONTIGS=true

Do you have any idea why this error might be happening. Any insight from you will be helpful.

Thanks and cheers,

Ana

[ricardo-aaron]

Wrote a comment under issue #27