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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Spend too long times to run hifiasm #647

Open hcph opened 4 months ago

hcph commented 4 months ago

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 commented 4 months ago

same question!!!

pashapu43 commented 3 months ago

same issue here!!

chhylp123 commented 3 months ago

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

hcph commented 3 months ago

@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 commented 2 months ago

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

chhylp123 commented 2 months ago

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.