Hu Jiang

Could you try to submit task `qsub -pe smp 5 -l vf=2.5G -o /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.o -e /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.e /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh` manually and see what happens?

If you are using `slurm` but the log show you are using `job_type: sge` SGE, so check what happened?

Hi, see [here](https://nextpolish.readthedocs.io/en/latest/OPTION.html#cmdoption-arg-submit) and [ParallelTask](https://github.com/moold/ParallelTask#configuration) to change the submit command template.

Hi, in generally, I do not recommend polishing using error-corrected reads, just use raw reads. The error-corrected reads may contain some bias errors (induced by error correction step). BTW, ~30-40x...

Hi, 2-3 iterations is ok, but the finally accuracy of an assembly is depending on short reads polishing.

Not exactly, I mean, if you want to get a high-accuracy genome, whether you polished it using long reads or not, you should polish the genome using short reads in...

Hi, could you paste the content of ` path/to/NextPolish.backup0/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e` to here?

As the log says, there is no `seq_split` execution file, so follow [here](https://nextpolish.readthedocs.io/en/latest/QSTART.html#installation) to reinstall. BTW, do not forget `make` command after downloading.

The RAM is too small

The computer node you submitted only have ~6Gb memory, you can not change it by adjusting parameters, you need to change another computer nodes to run it. EDITED: Maybe you...