chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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No further progress after generating *bin files #658

Open Iven-gif opened 5 months ago

Iven-gif commented 5 months ago

Hello,

I am using hifiasm 0.19.6-r595 to assemble an octoploid genome of approximately 7G. I plan to obtain the primary contigs (p_utg). I have used 400G of HiFi data and 295G of ONT data. My command is as follows:

hifiasm -o LA -t 64 -l 0 --primary --ul all_nano.fq.gz LAp.combined.hifi.fasta.gz

I ran the command on a PBS system with 1T of memory. The process has been running for 10 days. However, after generating four *bin files on the fourth day, there has been no further progress:

103938094427 May 28 06:43 LA.ec.bin
127946325584 May 28 06:59 LA.ovlp.reverse.bin
119110299392 May 28 06:51 LA.ovlp.source.bin
65670340936 May 28 09:25 LA.uidx.bin

Based on my previous experience, the next step should involve generating r_utg, followed by the bin files for the ONT data. However, no additional files have been generated, and the process status is "Sleep."

Is this behavior normal? Could it be due to the large data size? Any guidance would be greatly appreciated.

Thank you for your assistance.

Best regards, Iven

Iven-gif commented 5 months ago
top - 10:47:39 up 14 days, 18:34,  2 users,  load average: 63.68, 59.37, 60.95
Tasks: 1587 total,   1 running, 1586 sleeping,   0 stopped,   0 zombie
%Cpu(s): 48.5 us,  0.5 sy,  0.0 ni, 50.9 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem : 21133829+total, 13481768+free, 76302956+used,  2176356 buff/cacheKiB Swap: 67108860 total, 67108860 free,        0 used. 13483285+avail Mem 
   PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                                              
115465 stu_wan+  20   0  702.4g 662.6g   1264 S  6364 32.9 749797:26 hifiasm -o LA -t 64 -l 0 --primary --ul /public1/home/stu_wangbaiyu/workspace/Project/09.S_officinarum/LA/Data/ONT/a+
  9495 root      20   0  168032   4276   1976 R   3.4  0.0   0:00.44 top