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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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there is not enough disk space #37

Closed shehongbing closed 4 years ago

shehongbing commented 4 years ago

HI, I have 80G raw data and my disk space is 2T. Actually, it not enough disk space for me, so what should I do?

moold commented 4 years ago

Do you use this option: deltmp = yes? In theory, NextDenovo should not use 2T disk space for a normal genome with 80G raw data. But if you have set deltmp = yes, you can try to set minimap2_options_raw = -x ava-ont --minlen 1000.

shehongbing commented 4 years ago

Yes, I set the option deltmp = yes. It’s because there are about 270 raw_align files in /01.raw_align/02.raw_align.sh.work and each raw_align with 20G

在 2019年12月2日，上午9:19，Hu Jiang notifications@github.com 写道：

Do you use set this option: deltmp = yes? In theory, NextDenovo should not use 2T disk space for a normal genome with 80G raw data. But if you have set deltmp = yes, you can try to set minimap2_options_raw = -x ava-ont --minlen 1000.

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moold commented 4 years ago

It means your genome is a high repetitive genome, so pls try to use minimap2_options_raw = -x ava-ont --minlen 1000 to filter short repeat hits.

shehongbing commented 4 years ago

Hi, I try it. actually, it still need to about 6T disk space

moold commented 4 years ago

If you still want to reduce the disk space requirements, just increase --minlen.

shehongbing commented 4 years ago

Thank you

在 2019年12月11日，下午7:47，Hu Jiang notifications@github.com 写道：

If you still want to reduce the disk space requirements, just increase --minlen.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextDenovo/issues/37?email_source=notifications&email_token=ALZETBOAAP4GDP5SYXASOETQYDHOLA5CNFSM4JTLY7ZKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGS2VLY#issuecomment-564505263, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALZETBOHBJH6WQAT2I75PTDQYDHOLANCNFSM4JTLY7ZA.