NextPolish was core dumped in ‘01.lgs_polish/05.polish.ref.sh.work’ about nextpolish HOT 5 CLOSED

Hi, could you compare the result file 05.polish.ref.sh.work/polish_genome*/genome.nextpolish.part*.fasta and its input file input.genome.fasta to extract the un-polished sequence and its bam lgs.sort.bam using samtools view -b lgs.sort.bam $UN-POLISHED-SEQUENCE-NAME and send this data to me, so I can debug it, Thank you so much.

from nextpolish.

Thank you for your help. I uoload the data into 百度云.
链接：https://pan.baidu.com/s/1J9CFwBjqnX_utywjbTXnGA
提取码：lzt1

If you need more information, you can email me at [email protected].

from nextpolish.

I reassembled the data using Flye v2.7.1, and everything goes well. Thank you again!

from nextpolish.

Hi, actually, I have successfully run your data without any errors with nextPolish v1.2.1. While I found the length of your input genome is too short, it does not look like contigs but some reads. It may not be appropriate to use NextPolish to do the polish, instend, using NextDenovo or other similar tools to do the self-corrections may be better.

from nextpolish.

Thank you for your help! This data is a human gut metagenomic data. I found Flye v2.7.1 is the most suitable software. As per your recommendation, I will remove the sequences with length less than 2000 bp.

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