Open Iven-gif opened 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
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:
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