Comments (16)
Could you send the following two files to me by email ?
- /nextdenovo/01.correct/01.raw_align/03.sort_align.sh.work/sort_align006/input.seed.088.sorted.ovl
- /nextdenovo/01.correct/01.raw_align/.input.seed.088.idx
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OK
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Hi, I have checked files that your uploaded and it seems this is a old version bug, I have fixed in the new version some weeks ago, so pls download the newest version and try again.
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You should re-run all pipeline, not only the get_cns step.
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But, if you only have few tasks with this error, you can check the input.fofn for the sort task, such as: /nextdenovo/01.correct/01.raw_align/03.sort_align.sh.work/sort_align006/input.fofn, and rerurn the minimap task which produced the ovl files in input.fofn. and then re-run the corresponding sort task and cns task.
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We have used NextDenovo for lots of large genomes with genome size from 10G to 30G, for large genome size, you can check FAQ IV (use usetempdir option and adjust -k -w for minimap2). Actually, for large genomes , if you want to correct the raw reads and then do the assembly, you almost have no other choices, that is why we developed NextDenovo.
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I think you can re-run one sort task, and check if this is ok, and then re-run all other unfinished tasks.
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1.No, not only for pacbio data.
2. It means IO wait, please use usetempdir option, especially if usetempdir is on a SSD driver.
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I will close this issue, but if you still have this problem, feel free to reopen it.
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Related Issues (20)
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