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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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short reads polishing stopped for the second round #46

Open longzhangnation opened 4 years ago

longzhangnation commented 4 years ago

Hi, I am using Nextpolish for my genome , but it stopped at the second round of short reads polishing . I use the same code as the first round , and feed it with the sorted bam file . According to my experience , it will not take much time to polish genomes with short read , but I use 7 days and it still goes no further . My command is python /he_lab/share/data/local/NextPolish/lib/nextpolish1.py -g ./wtd_assem_short_pol1.fasta -t 1 -p 20 -s SGS_mapped_sorted2.bam -o wtd_assem_short_pol2.fasta . So can you give me some advice ?

moold commented 4 years ago

Some of sub-processes are crashed (usually caused by insufficient memory), which blocked the main process. This is a bug of multiprocess module in python. so you should kill the main task, and just rerun the main task. It it will skip corrected seqs and continue running.

longzhangnation commented 4 years ago

Maybe it is because of that . I will try again . Thank you .