Comments (6)
moold
commented on June 8, 2024
1
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.
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shehongbing
commented on June 8, 2024
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 ***@***.***> 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 on June 8, 2024
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.
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shehongbing
commented on June 8, 2024
Hi, I try it. actually, it still need to about 6T disk space
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moold
commented on June 8, 2024
If you still want to reduce the disk space requirements, just increase --minlen.
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shehongbing
commented on June 8, 2024
Thank you
… 在 2019年12月11日，下午7:47，Hu Jiang ***@***.***> 写道：
If you still want to reduce the disk space requirements, just increase --minlen.
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Related Issues (20)
- Only one sample or multiple samples can be used in nextdenovo? HOT 1
- Non-zero exit status 134 HOT 2
- [ERROR] failed to find seq file type or empty file after ctg_graph HOT 4
- Assembly is running around a month and going strong - or is it stalled? HOT 15
- about the ParallelTask for the nextdenovo HOT 1
- NextDenovo Parent Job Failed, No Error, Subtasks still running HOT 1
- Low performance with highly repeated regions HOT 1
- non-zero exit status 137, error info: . - assembly still finishes though HOT 1
- Unable to run test data on macOS HOT 4
- Samtools sort out-of-memory HOT 1
- Segmentation fault (core dumped) at 03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0 HOT 1
- Can you run nextDenovo without a config file? HOT 1
- TypeError: unsupported operand type(s) HOT 2
- long time for assemling genome HOT 6
- Can I assemble a gap free genome using only regular ONT data? HOT 1
- telomeres getting lost HOT 6
- [4501 ERROR] 2023-06-13 22:29:40 the input data is insufficient for an assembly. HOT 3
- No assembly file after running NextDenovo HOT 1
- sort_align step erro HOT 1
- Does NEXTDENOVO filter the contig before output? HOT 2
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