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inutano/wtdbg2.console.txt

Created July 25, 2019 08:53
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wtdbg2 genome assembly: output in console
Raw
wtdbg2.console.txt
$ ls ERR2092776_1.fastq
ERR2092776_1.fastq
$ docker run -it --rm -v $(pwd):/work -w /work quay.io/inutano/wtdbg2:v2.2 wtdbg2 -g95m -t 32 -i ERR2092776_1.fastq -fo worm.wtdbg2
--
-- total memory 65880284.0 kB
-- available 65173720.0 kB
-- 12 cores
-- Starting program: wtdbg2 -g95m -t 32 -i ERR2092776_1.fastq -fo worm.wtdbg2
-- pid 1
-- date Wed Jul 17 03:38:08 2019
--
[Wed Jul 17 03:38:08 2019] loading reads
583466 reads
[Wed Jul 17 03:41:27 2019] filtering from 583466 reads (>=0 bp), 8860671330 bp. Try selecting 4750000000 bp
[Wed Jul 17 03:41:29 2019] Done, 170475 reads (>=0 bp), 4750009856 bp, 18554647 bins
** PROC_STAT(0) **: real 201.259 sec, user 59.340 sec, sys 66.670 sec, maxrss 2656492.0 kB, maxvsize 3002756.0 kB
[Wed Jul 17 03:41:29 2019] Set --edge-cov to 3
KEY PARAMETERS: -k 0 -p 21 -K 1000.049988 -S 4.000000 -g 95000000 -X 50.000000 -e 3 -L 0
[Wed Jul 17 03:41:29 2019] generating nodes, 32 threads
[Wed Jul 17 03:41:31 2019] indexing bins[0,18554647] (4749989632 bp), 32 threads
[Wed Jul 17 03:41:33 2019] - scanning kmers (K0P21S4.00) from 18554647 bins
18554647 bins
********************** Kmer Frequency **********************
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********************** 1 - 201 **********************
Quatiles:
10% 20% 30% 40% 50% 60% 70% 80% 90% 95%
1 1 1 2 2 4 6 11 31 52
# If the kmer distribution is not good, please kill me and adjust -k, -p, and -K
# Cannot get a good distribution anyway, should adjust -S -s, also -A -e in assembly
** PROC_STAT(0) **: real 286.899 sec, user 705.130 sec, sys 142.910 sec, maxrss 9263368.0 kB, maxvsize 14197852.0 kB
[Wed Jul 17 03:42:55 2019] - high frequency kmer depth is set to 1000
[Wed Jul 17 03:42:58 2019] - Total kmers = 359942037
[Wed Jul 17 03:42:58 2019] - average kmer depth = 4
[Wed Jul 17 03:42:58 2019] - 247708725 low frequency kmers (<2)
[Wed Jul 17 03:42:58 2019] - 1071 high frequency kmers (>1000)
[Wed Jul 17 03:42:58 2019] - indexing 112232241 kmers, 479060133 instances (at most)
18554647 bins
[Wed Jul 17 03:44:00 2019] - indexed 112232241 kmers, 478808414 instances
[Wed Jul 17 03:44:00 2019] - masked 468 bins as closed
[Wed Jul 17 03:44:00 2019] - sorting
** PROC_STAT(0) **: real 353.480 sec, user 1446.380 sec, sys 187.150 sec, maxrss 9263368.0 kB, maxvsize 14197852.0 kB
[Wed Jul 17 03:44:02 2019] Done
170475 reads|total hits 6662405
** PROC_STAT(0) **: real 477.596 sec, user 2890.700 sec, sys 212.480 sec, maxrss 9263368.0 kB, maxvsize 14197852.0 kB
[Wed Jul 17 03:46:06 2019] chainning ... 2127777 hits into 991834, deleted 1821901 non-best hits between two reads
[Wed Jul 17 03:46:06 2019] picking best 500 hits for each read ... 4733333 hits
[Wed Jul 17 03:46:06 2019] clipping ... 1.99% bases
[Wed Jul 17 03:46:18 2019] generated 114742747 regs
[Wed Jul 17 03:46:19 2019] sorting regs ... Done
[Wed Jul 17 03:46:21 2019] generating intervals ... 4512196 intervals
[Wed Jul 17 03:46:22 2019] selecting important intervals from 4512196 intervals
[Wed Jul 17 03:47:45 2019] Intervals: kept 112713, discarded 4399483
** PROC_STAT(0) **: real 577.473 sec, user 3066.800 sec, sys 354.670 sec, maxrss 9263368.0 kB, maxvsize 14339852.0 kB
[Wed Jul 17 03:47:45 2019] Done, 112713 nodes
[Wed Jul 17 03:47:45 2019] output "worm.wtdbg2.1.nodes". Done.
[Wed Jul 17 03:47:59 2019] median node depth = 25
[Wed Jul 17 03:47:59 2019] masked 557 high coverage nodes (>200 or <3)
[Wed Jul 17 03:47:59 2019] masked 1042 repeat-like nodes by local subgraph analysis
[Wed Jul 17 03:47:59 2019] generating edges
[Wed Jul 17 03:48:07 2019] Done, 3498109 edges
[Wed Jul 17 03:48:07 2019] output "worm.wtdbg2.1.reads". Done.
[Wed Jul 17 03:48:13 2019] output "worm.wtdbg2.1.dot.gz". Done.
[Wed Jul 17 03:48:16 2019] graph clean
[Wed Jul 17 03:48:16 2019] rescued 517 low cov edges
[Wed Jul 17 03:48:16 2019] deleted 12 binary edges
[Wed Jul 17 03:48:16 2019] deleted 4173 isolated nodes
[Wed Jul 17 03:48:17 2019] cut 69091 transitive edges
[Wed Jul 17 03:48:17 2019] output "worm.wtdbg2.2.dot.gz". Done.
[Wed Jul 17 03:48:18 2019] 13983 bubbles; 3280 tips; 4 yarns;
[Wed Jul 17 03:48:18 2019] deleted 2633 isolated nodes
[Wed Jul 17 03:48:18 2019] output "worm.wtdbg2.3.dot.gz". Done.
[Wed Jul 17 03:48:18 2019] cut 31 branching nodes
[Wed Jul 17 03:48:18 2019] deleted 2 isolated nodes
[Wed Jul 17 03:48:18 2019] building unitigs
[Wed Jul 17 03:48:18 2019] TOT 115463168, CNT 556, AVG 207668, MAX 5787136, N50 2336000, L50 17, N90 577024, L90 52, Min 1536
[Wed Jul 17 03:48:18 2019] output "worm.wtdbg2.frg.nodes". Done.
[Wed Jul 17 03:48:18 2019] generating links
[Wed Jul 17 03:48:18 2019] generated 159 links
[Wed Jul 17 03:48:18 2019] output "worm.wtdbg2.frg.dot.gz". Done.
[Wed Jul 17 03:48:18 2019] rescue 0 weak links
[Wed Jul 17 03:48:18 2019] deleted 9 binary links
[Wed Jul 17 03:48:18 2019] cut 11 transitive links
[Wed Jul 17 03:48:18 2019] remove 6 boomerangs
[Wed Jul 17 03:48:18 2019] detached 1 repeat-associated paths
[Wed Jul 17 03:48:18 2019] remove 52 weak branches
[Wed Jul 17 03:48:18 2019] cut 3 tips
[Wed Jul 17 03:48:18 2019] pop 2 bubbles
[Wed Jul 17 03:48:18 2019] cut 0 tips
[Wed Jul 17 03:48:18 2019] output "worm.wtdbg2.ctg.dot.gz". Done.
[Wed Jul 17 03:48:18 2019] building contigs
[Wed Jul 17 03:48:19 2019] searched 483 contigs
[Wed Jul 17 03:48:19 2019] Estimated: TOT 113215488, CNT 211, AVG 536567, MAX 7316992, N50 3647744, L50 11, N90 1153792, L90 30, Min 5120
[Wed Jul 17 03:49:22 2019] output 211 contigs
[Wed Jul 17 03:49:25 2019] Program Done
** PROC_STAT(TOTAL) **: real 676.811 sec, user 3748.450 sec, sys 394.560 sec, maxrss 9263368.0 kB, maxvsize 14339852.0 kB
$ ls -l worm*
-rw-r--r-- 1 inutano staff 58057295 Jul 17 12:48 worm.wtdbg2.1.dot.gz
-rw-r--r-- 1 inutano staff 118366121 Jul 17 12:47 worm.wtdbg2.1.nodes
-rw-r--r-- 1 inutano staff 74388360 Jul 17 12:48 worm.wtdbg2.1.reads
-rw-r--r-- 1 inutano staff 3358409 Jul 17 12:48 worm.wtdbg2.2.dot.gz
-rw-r--r-- 1 inutano staff 2663266 Jul 17 12:48 worm.wtdbg2.3.dot.gz
-rw-r--r-- 1 inutano staff 242111506 Jul 17 12:46 worm.wtdbg2.alignments.gz
-rw-r--r-- 1 inutano staff 785 Jul 17 12:44 worm.wtdbg2.binkmer
-rw-r--r-- 1 inutano staff 15689 Jul 17 12:44 worm.wtdbg2.closed_bins
-rw-r--r-- 1 inutano staff 5802696 Jul 17 12:46 worm.wtdbg2.clps
-rw-r--r-- 1 inutano staff 16481 Jul 17 12:48 worm.wtdbg2.ctg.dot.gz
-rw-r--r-- 1 inutano staff 1268855529 Jul 17 12:49 worm.wtdbg2.ctg.lay.gz
-rw-r--r-- 1 inutano staff 183220 Jul 17 12:49 worm.wtdbg2.events
-rw-r--r-- 1 inutano staff 18993 Jul 17 12:48 worm.wtdbg2.frg.dot.gz
-rw-r--r-- 1 inutano staff 1640879 Jul 17 12:48 worm.wtdbg2.frg.nodes
-rw-r--r-- 1 inutano staff 650999 Jul 17 12:42 worm.wtdbg2.kmerdep
$ docker run -it --rm -v $(pwd):/work -w /work quay.io/inutano/wtdbg2:v2.2 wtpoa-cns -t 32 -i worm.wtdbg2.ctg.lay.gz -fo worm.wtdbg2.fa
--
-- total memory 65880284.0 kB
-- available 65128228.0 kB
-- 12 cores
-- Starting program: wtpoa-cns -t 32 -i worm.wtdbg2.ctg.lay.gz -fo worm.wtdbg2.fa
-- pid 1
-- date Wed Jul 17 03:55:13 2019
--
211 contigs 97245 edges
** PROC_STAT(TOTAL) **: real 1184.292 sec, user 13563.470 sec, sys 139.660 sec, maxrss 1882488.0 kB, maxvsize 3937212.0 kB
---
$ ls -l worm.wtdbg2.fa
-rw-r--r-- 1 inutano staff 111552736 Jul 17 13:14 worm.wtdbg2.fa
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