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Spend too long times to run hifiasm #647

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hcph opened this issue May 4, 2024 · 6 comments
Open

Spend too long times to run hifiasm #647

hcph opened this issue May 4, 2024 · 6 comments

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@hcph
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hcph commented May 4, 2024

Your tool is impressive, but I seem to be encountering an issue with the processing time. After executing the command:
hifiasm -o total_add.asm -t 150 --n-hap 6 --ul ont.sup.pass.fq.gz --ul-cut 500 --h1 hic_R1_clean.fq.gz --h2 hic_R2_clean.fq.gz Hifi_total.fastq.gz 2>hifiasmtotal_new2_nohup.txt &
I haven't received the contigs despite the command running for 6236425 hours. This delay has me quite concerned.

@ltachi11
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same question!!!

@pashapu43
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same issue here!!

@chhylp123
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@pashapu43 Could you please show the log file? Sorry for the late reply since I was quite busy this month.

@hcph
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hcph commented Jun 21, 2024

@pashapu43 Could you please show the log file? Sorry for the late reply since I was quite busy this month.
Thank you for your reply. The log file is as following. Could you please help me to find the problem?
hifiasmtotal_new2_nohup.txt

@Weihankk
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Weihankk commented Jun 27, 2024

same question and same status in the log. The final statu is [M::uidx_write] Index has been written.

@chhylp123
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I feel like sometimes hifiasm is just too slow. In this case, please just wait for the completion. Another possibility is there is not enough RAM.

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