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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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Slurm exit code 2 #54

Closed dagi34 closed 2 years ago

dagi34 commented 2 years ago

Hi, I am using Smartdenovo on a number of nodes. I installed it and carried out a run. However the run failed with exit code 2. I found that this means 'invalid usage of some shell built-in command. Examples of built-in commands include alias, echo, and printf'. Does it have dependencies which I do not know about please?

This is the .out file:

Running on nyquist PREFIX=smartdenovo_ONT

EXE_PRE=smartdenovo/wtpre EXE_ZMO=smartdenovo/wtzmo EXE_OBT=smartdenovo/wtobt EXE_GBO=smartdenovo/wtgbo EXE_CLP=smartdenovo/wtclp EXE_LAY=smartdenovo/wtlay EXE_CNS=smartdenovo/wtcns N_THREADS=24

all:$(PREFIX).dmo.cns

$(PREFIX).fa.gz: $(EXE_PRE) -J 5000 /opt/local/data/dagi1/ERR2173373.fastq | gzip -c -1 > $@

$(PREFIX).dmo.ovl:$(PREFIX).fa.gz $(EXE_ZMO) -t $(N_THREADS) -i $(PREFIX).fa.gz -fo $@ -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000

$(PREFIX).dmo.obt:$(PREFIX).fa.gz $(PREFIX).dmo.ovl $(EXE_CLP) -i $(PREFIX).dmo.ovl -fo $@ -d 3 -k 300 -m 0.1 -FT

$(PREFIX).dmo.lay:$(PREFIX).fa.gz $(PREFIX).dmo.obt $(PREFIX).dmo.ovl $(EXE_LAY) -i $(PREFIX).fa.gz -b $(PREFIX).dmo.obt -j $(PREFIX).dmo.ovl -fo $(PREFIX).dmo.lay -w 300 -s 200 -m 0.1 -r 0.95 -c 1

$(PREFIX).dmo.cns:$(PREFIX).dmo.lay $(EXE_CNS) -t $(N_THREADS) $< > $@ 2> $@.log

real 0m0.037s user 0m0.025s sys 0m0.005s make: smartdenovo_ONT.mak: No such file or directory make: *** No rule to make target 'smartdenovo_ONT.mak'. Stop.

real 0m0.009s user 0m0.006s sys 0m0.001s

and this is the text file to submit the job:

!/bin/bash

CPU and RAM resources

SBATCH --partition=teaching_cpu

SBATCH --ntasks=1

SBATCH --cpus-per-task=24

SBATCH --mem-per-cpu=6G

job parameters

SBATCH --job-name=smartdenovo_ONT_arabidopsis

email user

SBATCH --mail-user=dorita.galea@um.edu.mt

SBATCH --mail-type=all

# echo Running on $(hostname) #name not required source /opt/conda/etc/profile.d/conda.sh #activate conda env conda activate dorita_env1 cd /opt/local/data/dagi1/ #path to data file time smartdenovo/smartdenovo.pl -p smartdenovo_ONT -c 1 -t 24 /opt/local/data/dagi1/ERR2173373.fastq smartdenovo_ONT.mak time make -f smartdenovo_ONT.mak

ruanjue commented 2 years ago

Please check this code

time smartdenovo/smartdenovo.pl -p smartdenovo_ONT -c 1 -t 24 /opt/local/data/dagi1/ERR2173373.fastq smartdenovo_ONT.mak

Maybe you missed a >

dagi34 commented 2 years ago

Thanks. Regards

dagi34 commented 2 years ago

Thanks