ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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the estimate of running time #262

Closed ghost closed 1 year ago

ghost commented 1 year ago

Hello, I have run the wtdbg2 for one weeks, but I fonund that the program still work. Although the size of the lignmen.gz file continues to increase (so I think it's not a bug), I'm not sure how much longer it will take, and is it correct for the program to take so long?

And here is my output of my runnning log files,

--
-- total memory     1056465520.0 kB
-- available        1021266244.0 kB
-- 128 cores
-- Starting program: wtdbg2 -t 120 -x ccs -g 7.8g -o all_ccs -i /home/data/ycy/project/WNYCY/raw/WNYCY_PB/WN_YCY.ccs.fastq.gz -i /home/data/ycy/project/WNYCY/raw/WNYCY_PB/add/raw_data_2023-05-23/PB/CCS/D230400606A/m84070_230510_070023_s1/WNYCY_add.1.css.fastq.gz -i /home/data/ycy/project/WNYCY/raw/WNYCY_PB/add/raw_data_2023-05-23/PB/CCS/D230400606A/m84072_230421_093207_s2/WNYCY_add.2.css.fastq.gz -i /home/data/ycy/project/WNYCY/raw/WNYCY_PB/add/raw_data_2023-05-23/PB/CCS/D230400606A/m84072_230422_091801_s1/WNYCY_add.3.css.fastq.gz -i /home/data/ycy/project/WNYCY/raw/WNYCY_PB/add/raw_data_2023-05-25/PB/CSS/WNYCY-1/m84070_230426_101715_s3/WNYCY_add.4.css.fastq.gz
-- pid                   3803477
-- date         Tue Jul  4 11:23:52 2023
--
[Tue Jul  4 11:23:52 2023] loading reads
47207232 reads
[Tue Jul  4 14:52:53 2023] filtering from 47207232 reads (>=0 bp), 720814765601 bp. Try selecting 390000000000 bp
[Tue Jul  4 14:53:41 2023] Done, 17101415 reads (>=0 bp), 390000003328 bp, 1523437446 bins
** PROC_STAT(0) **: real 12588.969 sec, user 13617.330 sec, sys 4063.160 sec, maxrss 194534260.0 kB, maxvsize 204577192.0 kB
[Tue Jul  4 14:53:41 2023] Set --edge-cov to 3
KEY PARAMETERS: -k 0 -p 21 -K 0.050000 -A -S 4.000000 -s 0.500000 -g 7800000000 -X 50.000000 -e 3 -L 0
[Tue Jul  4 14:53:41 2023] generating nodes, 120 threads
[Tue Jul  4 14:53:41 2023] indexing bins[(0,1523437446)/1523437446] (389999986176/714795222272 bp), 120 threads
[Tue Jul  4 14:53:42 2023] - scanning kmers (K0P21S4.00) from 1523437446 bins
1523437446 bins
********************** Kmer Frequency **********************
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**********************     1 - 201    **********************
Quatiles:
   10%   20%   30%   40%   50%   60%   70%   80%   90%   95%
    53    93   191   486  1500  4525 12857 35176 65535 65535
** PROC_STAT(0) **: real 13094.153 sec, user 58399.520 sec, sys 4536.840 sec, maxrss 203889764.0 kB, maxvsize 222450504.0 kB
[Tue Jul  4 15:02:06 2023] - high frequency kmer depth is set to 65535
[Tue Jul  4 15:02:06 2023] - Total kmers = 394487863
[Tue Jul  4 15:02:06 2023] - average kmer depth = 133
[Tue Jul  4 15:02:06 2023] - 24284805 low frequency kmers (<2)
[Tue Jul  4 15:02:06 2023] - 0 high frequency kmers (>65535)
[Tue Jul  4 15:02:06 2023] - indexing 370306689 kmers, 49408689641 instances (at most)
1523437446 bins
[Tue Jul  4 15:15:28 2023] - indexed  370306689 kmers, 49374195213 instances
[Tue Jul  4 15:15:35 2023] - masked 7772 bins as closed
[Tue Jul  4 15:15:35 2023] - sorting
** PROC_STAT(0) **: real 13977.087 sec, user 149773.120 sec, sys 6284.070 sec, maxrss 494622904.0 kB, maxvsize 516140856.0 kB
[Tue Jul  4 15:16:49 2023] **Done**
ghost commented 1 year ago

I’ve finished it, and the program spent 13 days to assemble the genome.