No Consensus ctg.fa file created

[lucyintheskyzzz]

Hi I am running wtdbg2 on my viral metagenomics shotgun fastq files 56k reads. I was able to assemble long reads, but was unable to create a consensus ctg.fa file. What do you recommend running for low long read fastq files?

-- Starting program: ./wtdbg2 -x ont -g 1m -i /lustre/project/taw/ONR012021/fastq_concat/barcode01.fastq -fo ONR012021barcode01 -S 1
-- pid 103006
-- date Wed Jan 4 16:42:43 2023

[Wed Jan 4 16:42:43 2023] loading reads
0 reads
[Wed Jan 4 16:42:43 2023] Done, 0 reads (>=5000 bp), 0 bp, 0 bins
** PROC_STAT(0) **: real 0.409 sec, user 0.340 sec, sys 0.120 sec, maxrss 42188.0 kB, maxvsize 190588.0 kB
[Wed Jan 4 16:42:43 2023] Set --edge-cov to 2
KEY PARAMETERS: -k 15 -p 0 -K 1000.049988 -A -S 1.000000 -s 0.050000 -g 1000000 -X 50.000000 -e 2 -L 5000
[Wed Jan 4 16:42:43 2023] generating nodes, 4 threads
[Wed Jan 4 16:42:43 2023] indexing bins[(0,0)/0] (0/0 bp), 4 threads
[Wed Jan 4 16:42:43 2023] - scanning kmers (K15P0S1.00) from 0 bins
0 bins
********************** Kmer Frequency **********************

********************** 1 - 201 **********************
Quatiles:
10% 20% 30% 40% 50% 60% 70% 80% 90% 95%
0 0 0 0 0 0 0 0 0 0
** PROC_STAT(0) **: real 0.509 sec, user 0.360 sec, sys 0.150 sec, maxrss 65340.0 kB, maxvsize 414948.0 kB
[Wed Jan 4 16:42:44 2023] - high frequency kmer depth is set to 65535
[Wed Jan 4 16:42:44 2023] - Total kmers = 0
[Wed Jan 4 16:42:44 2023] - average kmer depth = 0
[Wed Jan 4 16:42:44 2023] - 0 low frequency kmers (<2)
[Wed Jan 4 16:42:44 2023] - 0 high frequency kmers (>65535)
[Wed Jan 4 16:42:44 2023] - indexing 0 kmers, 0 instances (at most)
0 bins
[Wed Jan 4 16:42:44 2023] - indexed 0 kmers, 0 instances
[Wed Jan 4 16:42:44 2023] - masked 0 bins as closed
[Wed Jan 4 16:42:44 2023] - sorting
** PROC_STAT(0) **: real 0.509 sec, user 0.360 sec, sys 0.150 sec, maxrss 65340.0 kB, maxvsize 414948.0 kB
[Wed Jan 4 16:42:44 2023] Done
0 reads|total hits 0
** PROC_STAT(0) **: real 0.609 sec, user 0.430 sec, sys 0.180 sec, maxrss 68192.0 kB, maxvsize 414948.0 kB
[Wed Jan 4 16:42:44 2023] sorting rdhits ... Done
[Wed Jan 4 16:42:44 2023] clipping ... -nan% bases
[Wed Jan 4 16:42:44 2023] generating regs ... 0
[Wed Jan 4 16:42:44 2023] sorting regs ... Done
[Wed Jan 4 16:42:44 2023] generating intervals ... 0 intervals
[Wed Jan 4 16:42:44 2023] selecting important intervals from 0 intervals
[Wed Jan 4 16:42:44 2023] Intervals: kept 0, discarded 0
** PROC_STAT(0) **: real 0.609 sec, user 0.430 sec, sys 0.180 sec, maxrss 68192.0 kB, maxvsize 414948.0 kB
[Wed Jan 4 16:42:44 2023] Done, 0 nodes
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.1.nodes". Done.
[Wed Jan 4 16:42:44 2023] median node depth = 0
[Wed Jan 4 16:42:44 2023] masked 0 high coverage nodes (>200 or <2)
[Wed Jan 4 16:42:44 2023] masked 0 repeat-like nodes by local subgraph analysis
[Wed Jan 4 16:42:44 2023] generating edges
[Wed Jan 4 16:42:44 2023] Done, 1 edges
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.1.reads". Done.
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.1.dot.gz". Done.
[Wed Jan 4 16:42:44 2023] graph clean
[Wed Jan 4 16:42:44 2023] rescued 0 low cov edges
[Wed Jan 4 16:42:44 2023] deleted 0 binary edges
[Wed Jan 4 16:42:44 2023] deleted 0 isolated nodes
[Wed Jan 4 16:42:44 2023] cut 0 transitive edges
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.2.dot.gz". Done.
[Wed Jan 4 16:42:44 2023] deleted 0 isolated nodes
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.3.dot.gz". Done.
[Wed Jan 4 16:42:44 2023] cut 0 branching nodes
[Wed Jan 4 16:42:44 2023] deleted 0 isolated nodes
[Wed Jan 4 16:42:44 2023] building unitigs
[Wed Jan 4 16:42:44 2023]
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.frg.nodes". Done.
[Wed Jan 4 16:42:44 2023] generating links
[Wed Jan 4 16:42:44 2023] generated 1 links
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.frg.dot.gz". Done.
[Wed Jan 4 16:42:44 2023] rescue 0 weak links
[Wed Jan 4 16:42:44 2023] deleted 0 binary links
[Wed Jan 4 16:42:44 2023] cut 0 transitive links
[Wed Jan 4 16:42:44 2023] remove 0 boomerangs
[Wed Jan 4 16:42:44 2023] remove 0 weak branches
[Wed Jan 4 16:42:44 2023] cut 0 tips
[Wed Jan 4 16:42:44 2023] pop 0 bubbles
[Wed Jan 4 16:42:44 2023] detached 0 repeat-associated paths
[Wed Jan 4 16:42:44 2023] cut 0 tips
[Wed Jan 4 16:42:44 2023] output "ONR012021barcode01.ctg.dot.gz". Done.
[Wed Jan 4 16:42:44 2023] building contigs
[Wed Jan 4 16:42:44 2023] searched 0 contigs
[Wed Jan 4 16:42:44 2023] Estimated:
[Wed Jan 4 16:42:44 2023] output 0 contigs
[Wed Jan 4 16:42:44 2023] Program Done
** PROC_STAT(TOTAL) **: real 0.838 sec, user 0.470 sec, sys 0.210 sec, maxrss 68192.0 kB, maxvsize 469584.0 kB

[lucyintheskyzzz]

So looks like I initially did not generate any contigs. I tried a different code from looking at other issues on here:

[kvigil@cypress01-079 wtdbg2]$ ./wtdbg2 -x ont -g 500k -e -S 0.5 -L 0 -i /lustre/project/taw/ONR012021/fastq_concat/barcode01.fastq -t8 -fo wtdbg2 -o /lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01 -l 512 -m 50 ont
WARNING: unused command-line arguments. For multiple input files, please apply multiple -i.
WARNING: try to recognize and add to input files list

-- total memory 264060460.0 kB
-- available 259681220.0 kB
-- 20 cores
-- Starting program: ./wtdbg2 -x ont -g 500k -e -S -L 0 -i /lustre/project/taw/ONR012021/fastq_concat/barcode01.fastq -t8 -fo wtdbg2 -o /lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01 -l 512 -m 50 0.5 ont
-- pid 40768
-- date Thu Jan 5 10:50:29 2023

[Thu Jan 5 10:50:29 2023] loading reads
55986 reads
[Thu Jan 5 10:50:29 2023] filtering from 55986 reads (>=0 bp), 52712377 bp. Try selecting 25000000 bp
[Thu Jan 5 10:50:30 2023] Done, 23703 reads (>=0 bp), 25000192 bp, 97654 bins
** PROC_STAT(0) **: real 0.601 sec, user 0.570 sec, sys 0.090 sec, maxrss 64248.0 kB, maxvsize 212904.0 kB
[Thu Jan 5 10:50:30 2023] Set --edge-cov to 3
KEY PARAMETERS: -k 15 -p 0 -K 1000.049988 -A -S 2.000000 -s 0.050000 -g 500000 -X 50.000000 -e 3 -L 0
[Thu Jan 5 10:50:30 2023] generating nodes, 8 threads
[Thu Jan 5 10:50:30 2023] indexing bins[(0,97654)/97654] (24999424/45649408 bp), 8 threads
[Thu Jan 5 10:50:30 2023] - scanning kmers (K15P0S2.00) from 97654 bins
97654 bins
********************** Kmer Frequency **********************
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********************** 1 - 201 **********************
Quatiles:
10% 20% 30% 40% 50% 60% 70% 80% 90% 95%
1 1 3 8 23 66 216 774 1424 2256
** PROC_STAT(0) **: real 1.503 sec, user 3.810 sec, sys 0.250 sec, maxrss 188620.0 kB, maxvsize 800024.0 kB
[Thu Jan 5 10:50:30 2023] - high frequency kmer depth is set to 2512
[Thu Jan 5 10:50:30 2023] - Total kmers = 3578396
[Thu Jan 5 10:50:30 2023] - average kmer depth = 10
[Thu Jan 5 10:50:30 2023] - 2758458 low frequency kmers (<2)
[Thu Jan 5 10:50:30 2023] - 116 high frequency kmers (>2512)
[Thu Jan 5 10:50:30 2023] - indexing 819822 kmers, 8852321 instances (at most)
97654 bins
[Thu Jan 5 10:50:31 2023] - indexed 819822 kmers, 8846294 instances
[Thu Jan 5 10:50:31 2023] - masked 89 bins as closed
[Thu Jan 5 10:50:31 2023] - sorting
** PROC_STAT(0) **: real 2.304 sec, user 7.860 sec, sys 0.470 sec, maxrss 245516.0 kB, maxvsize 882856.0 kB
[Thu Jan 5 10:50:31 2023] Done
23702 reads|total hits 19019875
** PROC_STAT(0) **: real 32.752 sec, user 321.980 sec, sys 2.830 sec, maxrss 877272.0 kB, maxvsize 2480260.0 kB
[Thu Jan 5 10:51:02 2023] sorting rdhits ... Done
[Thu Jan 5 10:51:03 2023] clipping ... 0.63% bases
[Thu Jan 5 10:51:03 2023] generating regs ... 4579204
[Thu Jan 5 10:51:05 2023] sorting regs ... Done
[Thu Jan 5 10:51:05 2023] generating intervals ... 18549 intervals
[Thu Jan 5 10:51:05 2023] selecting important intervals from 18549 intervals
[Thu Jan 5 10:51:05 2023] Intervals: kept 133, discarded 18416
** PROC_STAT(0) **: real 36.158 sec, user 333.500 sec, sys 2.990 sec, maxrss 899072.0 kB, maxvsize 2515620.0 kB
[Thu Jan 5 10:51:05 2023] Done, 133 nodes
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.1.nodes". Done.
[Thu Jan 5 10:51:05 2023] median node depth = 7
[Thu Jan 5 10:51:05 2023] masked 23 high coverage nodes (>200 or <3)
[Thu Jan 5 10:51:05 2023] masked 0 repeat-like nodes by local subgraph analysis
[Thu Jan 5 10:51:05 2023] generating edges
[Thu Jan 5 10:51:05 2023] Done, 11 edges
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.1.reads". Done.
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.1.dot.gz". Done.
[Thu Jan 5 10:51:05 2023] graph clean
[Thu Jan 5 10:51:05 2023] rescued 0 low cov edges
[Thu Jan 5 10:51:05 2023] deleted 0 binary edges
[Thu Jan 5 10:51:05 2023] deleted 110 isolated nodes
[Thu Jan 5 10:51:05 2023] cut 0 transitive edges
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.2.dot.gz". Done.
[Thu Jan 5 10:51:05 2023] deleted 0 isolated nodes
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.3.dot.gz". Done.
[Thu Jan 5 10:51:05 2023] cut 0 branching nodes
[Thu Jan 5 10:51:05 2023] deleted 0 isolated nodes
[Thu Jan 5 10:51:05 2023] building unitigs
[Thu Jan 5 10:51:05 2023]
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.frg.nodes". Done.
[Thu Jan 5 10:51:05 2023] generating links
[Thu Jan 5 10:51:05 2023] generated 1 links
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.frg.dot.gz". Done.
[Thu Jan 5 10:51:05 2023] rescue 0 weak links
[Thu Jan 5 10:51:05 2023] deleted 0 binary links
[Thu Jan 5 10:51:05 2023] cut 0 transitive links
[Thu Jan 5 10:51:05 2023] remove 0 boomerangs
[Thu Jan 5 10:51:05 2023] remove 0 weak branches
[Thu Jan 5 10:51:05 2023] cut 0 tips
[Thu Jan 5 10:51:05 2023] pop 0 bubbles
[Thu Jan 5 10:51:05 2023] detached 0 repeat-associated paths
[Thu Jan 5 10:51:05 2023] cut 0 tips
[Thu Jan 5 10:51:05 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode01.ctg.dot.gz". Done.
[Thu Jan 5 10:51:05 2023] building contigs
[Thu Jan 5 10:51:05 2023] searched 0 contigs
[Thu Jan 5 10:51:05 2023] Estimated:
[Thu Jan 5 10:51:05 2023] output 0 contigs
[Thu Jan 5 10:51:05 2023] Program Done
** PROC_STAT(TOTAL) **: real 36.358 sec, user 333.740 sec, sys 3.060 sec, maxrss 899072.0 kB, maxvsize 2515620.0 kB

[ruanjue]

[Wed Jan 4 16:42:43 2023] Done, 0 reads (>=5000 bp), 0 bp, 0 bins

The key problem was all of your reads have length less than 5kb, so please set -L 0 instead.

[lucyintheskyzzz]

Thanks Here is the result for my largest file size 655MB. These files are from my virus metagenomic sequencing. Is it possible to get wtdbg2 to run for low coverage viral metagenomic sequences? Is there a cut off value? Thanks!

total memory 264060460.0 kB
-- available 259577784.0 kB
-- 20 cores
-- Starting program: ./wtdbg2 -x ont -L 0 -i /lustre/project/taw/ONR012021/fastq_concat/barcode03.fastq -fo wtdbg2 -o /lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03 --edge-min 1 --rescue-low-cov-edges –t 4
-- pid 59909
-- date Fri Jan 6 10:58:44 2023

[Fri Jan 6 10:58:44 2023] loading reads
393887 reads
[Fri Jan 6 10:58:48 2023] Done, 393887 reads (>=0 bp), 293673350 bp, 948629 bins
** PROC_STAT(0) **: real 4.007 sec, user 3.310 sec, sys 0.730 sec, maxrss 198252.0 kB, maxvsize 349256.0 kB
KEY PARAMETERS: -k 0 -p 19 -K 1000.049988 -A -S 2.000000 -s 0.050000 -g 0 -X 50.000000 -e 1 -L 0
[Fri Jan 6 10:58:48 2023] generating nodes, 4 threads
[Fri Jan 6 10:58:48 2023] indexing bins[(0,948629)/948629] (242849024/242849024 bp), 4 threads
[Fri Jan 6 10:58:48 2023] - scanning kmers (K0P19S2.00) from 948629 bins
948629 bins
********************** Kmer Frequency **********************
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********************** 1 - 201 **********************
Quatiles:
10% 20% 30% 40% 50% 60% 70% 80% 90% 95%
1 1 5 20 82 326 1522 3889 14045 29551
** PROC_STAT(0) **: real 11.627 sec, user 26.760 sec, sys 2.090 sec, maxrss 632708.0 kB, maxvsize 968196.0 kB
[Fri Jan 6 10:58:55 2023] - high frequency kmer depth is set to 31827
[Fri Jan 6 10:58:55 2023] - Total kmers = 19819949
[Fri Jan 6 10:58:55 2023] - average kmer depth = 13
[Fri Jan 6 10:58:55 2023] - 15540841 low frequency kmers (<2)
[Fri Jan 6 10:58:55 2023] - 46 high frequency kmers (>31827)
[Fri Jan 6 10:58:55 2023] - indexing 4279062 kmers, 58912330 instances (at most)
948629 bins
[Fri Jan 6 10:59:04 2023] - indexed 4279062 kmers, 58894191 instances
[Fri Jan 6 10:59:04 2023] - masked 346 bins as closed
[Fri Jan 6 10:59:04 2023] - sorting
** PROC_STAT(0) **: real 21.446 sec, user 58.320 sec, sys 3.160 sec, maxrss 880516.0 kB, maxvsize 1234284.0 kB
[Fri Jan 6 10:59:05 2023] Done
384943 reads|total hits 453
** PROC_STAT(0) **: real 3924.607 sec, user 15458.000 sec, sys 1039.430 sec, maxrss 880516.0 kB, maxvsize 1234284.0 kB
[Fri Jan 6 12:04:08 2023] sorting rdhits ... Done
[Fri Jan 6 12:04:08 2023] clipping ... 99.74% bases
[Fri Jan 6 12:04:09 2023] generating regs ... 1591
[Fri Jan 6 12:04:09 2023] sorting regs ... Done
[Fri Jan 6 12:04:09 2023] generating intervals ... 565 intervals
[Fri Jan 6 12:04:09 2023] selecting important intervals from 565 intervals
[Fri Jan 6 12:04:09 2023] Intervals: kept 214, discarded 351
** PROC_STAT(0) **: real 3925.107 sec, user 15458.340 sec, sys 1039.550 sec, maxrss 880516.0 kB, maxvsize 1234284.0 kB
[Fri Jan 6 12:04:09 2023] Done, 214 nodes
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.1.nodes". Done.
[Fri Jan 6 12:04:09 2023] median node depth = 2
[Fri Jan 6 12:04:09 2023] masked 0 high coverage nodes (>200 or <1)
[Fri Jan 6 12:04:09 2023] masked 23 repeat-like nodes by local subgraph analysis
[Fri Jan 6 12:04:09 2023] generating edges
[Fri Jan 6 12:04:09 2023] Done, 86 edges
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.1.reads". Done.
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.1.dot.gz". Done.
[Fri Jan 6 12:04:09 2023] graph clean
[Fri Jan 6 12:04:09 2023] rescued 0 low cov edges
[Fri Jan 6 12:04:09 2023] deleted 0 binary edges
[Fri Jan 6 12:04:09 2023] deleted 44 isolated nodes
[Fri Jan 6 12:04:09 2023] cut 0 transitive edges
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.2.dot.gz". Done.
[Fri Jan 6 12:04:09 2023] 0 bubbles; 12 tips; 0 yarns; rescued 0 high edges
[Fri Jan 6 12:04:09 2023] deleted 2 isolated nodes
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.3.dot.gz". Done.
[Fri Jan 6 12:04:09 2023] cut 0 branching nodes
[Fri Jan 6 12:04:09 2023] deleted 0 isolated nodes
[Fri Jan 6 12:04:09 2023] building unitigs
[Fri Jan 6 12:04:09 2023] TOT 137728, CNT 65, AVG 2119, MAX 3584, N50 2048, L50 31, N90 1792, L90 58, Min 1792
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.frg.nodes". Done.
[Fri Jan 6 12:04:09 2023] generating links
[Fri Jan 6 12:04:09 2023] generated 1 links
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.frg.dot.gz". Done.
[Fri Jan 6 12:04:09 2023] rescue 0 weak links
[Fri Jan 6 12:04:09 2023] deleted 2 binary links
[Fri Jan 6 12:04:09 2023] cut 0 transitive links
[Fri Jan 6 12:04:09 2023] remove 0 boomerangs
[Fri Jan 6 12:04:09 2023] remove 0 weak branches
[Fri Jan 6 12:04:09 2023] cut 0 tips
[Fri Jan 6 12:04:09 2023] pop 0 bubbles
[Fri Jan 6 12:04:09 2023] detached 0 repeat-associated paths
[Fri Jan 6 12:04:09 2023] cut 0 tips
[Fri Jan 6 12:04:09 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONR012021/barcode03.ctg.dot.gz". Done.
[Fri Jan 6 12:04:09 2023] building contigs
[Fri Jan 6 12:04:09 2023] searched 65 contigs
[Fri Jan 6 12:04:09 2023] Estimated:
[Fri Jan 6 12:04:09 2023] output 0 contigs
[Fri Jan 6 12:04:09 2023] Program Done
** PROC_STAT(TOTAL) **: real 3925.808 sec, user 15458.770 sec, sys 1039.660 sec, maxrss 880516.0 kB, maxvsize 1234284.0 kB

[ruanjue]

If seq depth less than 20X, the assembly will be very bad. Also pay atention to --ctg-min-length and --ctg-min-nodes, when your targeted genomes are very small.

[lucyintheskyzzz]

Hi, I loaded a bigger fastq file and this is what I got:

(/lustre/project/taw/share/conda-envs/flye) [kvigil@cypress01-119 wtdbg2]$ ./wtdbg2 -x ont -g 1m -i /lustre/project/taw/ONRdolphinfecespooled/concatenate/dolphinfeces.fastq -fo wtdbg2 -o /lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq -L 0

-- total memory 65879704.0 kB
-- available 56531472.0 kB
-- 20 cores
-- Starting program: ./wtdbg2 -x ont -g 1m -i /lustre/project/taw/ONRdolphinfecespooled/concatenate/dolphinfeces.fastq -fo wtdbg2 -o /lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq -L 0
-- pid 38365
-- date Mon Jan 9 12:55:37 2023

[Mon Jan 9 12:55:37 2023] loading reads
980126 reads
[Mon Jan 9 12:55:45 2023] filtering from 980126 reads (>=0 bp), 693815770 bp. Try selecting 50000000 bp
[Mon Jan 9 12:55:45 2023] Done, 34049 reads (>=0 bp), 50000896 bp, 195311 bins
** PROC_STAT(0) **: real 7.917 sec, user 8.220 sec, sys 1.100 sec, maxrss 305812.0 kB, maxvsize 455792.0 kB
[Mon Jan 9 12:55:45 2023] Set --edge-cov to 3
KEY PARAMETERS: -k 15 -p 0 -K 1000.049988 -A -S 2.000000 -s 0.050000 -g 1000000 -X 50.000000 -e 3 -L 0
[Mon Jan 9 12:55:45 2023] generating nodes, 4 threads
[Mon Jan 9 12:55:45 2023] indexing bins[(0,195311)/195311] (49999616/568338688 bp), 4 threads
[Mon Jan 9 12:55:46 2023] - scanning kmers (K15P0S2.00) from 195311 bins
195311 bins
********************** Kmer Frequency **********************
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********************** 1 - 201 **********************
Quatiles:
10% 20% 30% 40% 50% 60% 70% 80% 90% 95%
1 1 1 3 8 27 105 330 713 1932
** PROC_STAT(0) **: real 11.356 sec, user 19.170 sec, sys 2.450 sec, maxrss 512080.0 kB, maxvsize 855604.0 kB
[Mon Jan 9 12:55:49 2023] - high frequency kmer depth is set to 3847
[Mon Jan 9 12:55:49 2023] - Total kmers = 9206144
[Mon Jan 9 12:55:49 2023] - average kmer depth = 9
[Mon Jan 9 12:55:49 2023] - 7575530 low frequency kmers (<2)
[Mon Jan 9 12:55:49 2023] - 91 high frequency kmers (>3847)
[Mon Jan 9 12:55:49 2023] - indexing 1630523 kmers, 14995628 instances (at most)
195311 bins
[Mon Jan 9 12:55:51 2023] - indexed 1630523 kmers, 14816226 instances
[Mon Jan 9 12:55:51 2023] - masked 287 bins as closed
[Mon Jan 9 12:55:51 2023] - sorting
** PROC_STAT(0) **: real 14.365 sec, user 30.540 sec, sys 3.350 sec, maxrss 609580.0 kB, maxvsize 950436.0 kB
[Mon Jan 9 12:55:52 2023] Done
34048 reads|total hits 4502
** PROC_STAT(0) **: real 167.887 sec, user 622.290 sec, sys 57.750 sec, maxrss 609580.0 kB, maxvsize 950436.0 kB
[Mon Jan 9 12:58:25 2023] sorting rdhits ... Done
[Mon Jan 9 12:58:25 2023] clipping ... 95.54% bases
[Mon Jan 9 12:58:25 2023] generating regs ... 16639
[Mon Jan 9 12:58:25 2023] sorting regs ... Done
[Mon Jan 9 12:58:25 2023] generating intervals ... 2035 intervals
[Mon Jan 9 12:58:25 2023] selecting important intervals from 2035 intervals
[Mon Jan 9 12:58:25 2023] Intervals: kept 220, discarded 1815
** PROC_STAT(0) **: real 167.988 sec, user 622.360 sec, sys 57.780 sec, maxrss 609580.0 kB, maxvsize 950436.0 kB
[Mon Jan 9 12:58:25 2023] Done, 220 nodes
[Mon Jan 9 12:58:25 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.1.nodes". Done.
[Mon Jan 9 12:58:25 2023] median node depth = 5
[Mon Jan 9 12:58:25 2023] masked 0 high coverage nodes (>200 or <3)
[Mon Jan 9 12:58:25 2023] masked 4 repeat-like nodes by local subgraph analysis
[Mon Jan 9 12:58:25 2023] generating edges
[Mon Jan 9 12:58:25 2023] Done, 150 edges
[Mon Jan 9 12:58:25 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.1.reads". Done.
[Mon Jan 9 12:58:25 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.1.dot.gz". Done.
[Mon Jan 9 12:58:25 2023] graph clean
[Mon Jan 9 12:58:25 2023] rescued 0 low cov edges
[Mon Jan 9 12:58:25 2023] deleted 0 binary edges
[Mon Jan 9 12:58:25 2023] deleted 95 isolated nodes
[Mon Jan 9 12:58:25 2023] cut 0 transitive edges
[Mon Jan 9 12:58:25 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.2.dot.gz". Done.
[Mon Jan 9 12:58:25 2023] deleted 0 isolated nodes
[Mon Jan 9 12:58:25 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.3.dot.gz". Done.
[Mon Jan 9 12:58:25 2023] cut 0 branching nodes
[Mon Jan 9 12:58:25 2023] deleted 0 isolated nodes
[Mon Jan 9 12:58:25 2023] building unitigs
[Mon Jan 9 12:58:25 2023] TOT 123136, CNT 60, AVG 2053, MAX 3072, N50 2048, L50 29, N90 1792, L90 53, Min 1280
[Mon Jan 9 12:58:25 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.frg.nodes". Done.
[Mon Jan 9 12:58:26 2023] generating links
[Mon Jan 9 12:58:26 2023] generated 1 links
[Mon Jan 9 12:58:26 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.frg.dot.gz". Done.
[Mon Jan 9 12:58:26 2023] rescue 0 weak links
[Mon Jan 9 12:58:26 2023] deleted 2 binary links
[Mon Jan 9 12:58:26 2023] cut 0 transitive links
[Mon Jan 9 12:58:26 2023] remove 0 boomerangs
[Mon Jan 9 12:58:26 2023] remove 0 weak branches
[Mon Jan 9 12:58:26 2023] cut 0 tips
[Mon Jan 9 12:58:26 2023] pop 0 bubbles
[Mon Jan 9 12:58:26 2023] detached 0 repeat-associated paths
[Mon Jan 9 12:58:26 2023] cut 0 tips
[Mon Jan 9 12:58:26 2023] output "/lustre/project/taw/share/apps/wtdbg2/ONRdolphinfecespooled/dolphinfeces.fastq.ctg.dot.gz". Done.
[Mon Jan 9 12:58:26 2023] building contigs
[Mon Jan 9 12:58:26 2023] searched 60 contigs
[Mon Jan 9 12:58:26 2023] Estimated:
[Mon Jan 9 12:58:26 2023] output 0 contigs
[Mon Jan 9 12:58:26 2023] Program Done
** PROC_STAT(TOTAL) **: real 168.406 sec, user 622.490 sec, sys 57.890 sec, maxrss 609580.0 kB, maxvsize 950436.0 kB

(/lustre/project/taw/share/conda-envs/flye) [kvigil@cypress01-119 wtdbg2]$