sjackman
commented
6 years ago Use ntCard to count the number of distinct 32-mers in the data set. With that value in hand, we can predict the memory usage of ABySS. https://github.com/bcgsc/ntCard
Open kokyriakidis opened 6 years ago
sjackman
commented
6 years ago Use ntCard to count the number of distinct 32-mers in the data set. With that value in hand, we can predict the memory usage of ABySS. https://github.com/bcgsc/ntCard
kmnip
commented
6 years ago @kokyriakidis Since you are using a small k-mer size (ie. 32), I would recommend recompiling ABySS with a smaller max kmer size. The default is 128, which is 4 times as much memory than needed.
Reconfigure from source with this command and then re-compile:
./configure --enable-maxk=32By the way, Trans-ABySS is actually not using the Bloom filter de bruijn graph implementation of ABySS.
sjackman
commented
6 years ago The easiest way to install ABySS with a different value of maxk is to use Linuxbrew.
Install Linuxbrew https://linuxbrew.sh
brew tap brewsci/bio
brew edit abyss
# Change --enable-maxk=128 to --enable-maxk=32
brew install -s abyss
kokyriakidis
commented
6 years ago So let me ask you something. Let’s say I compile abyss with maxk=512 in a machine and in an other machine I compile abyss with kmax=90. If I run the same commands with k=32 and with the same input files, am I gonna have different memory usage results?
sjackman
commented
6 years ago Yes, --enable-maxk=512 will use 16 times the memory as --enable-maxk=32.
kokyriakidis
commented
6 years ago Ok I will try it and I will tell you my results. Keep it open.
One more question. If I iterate from 32 to 90 by 2 and in a second machine (with the same maxk) iterate from 32 to 90 by 1, will I have the same result at k=40 for example? Or the number of previous iterations have an impact on the result?
kmnip
commented
6 years ago If you assemble at k=40 on different machines:
However, the merged assembly of 32-90:1 would not be the same as the merged assembly of 32-90:2.
kokyriakidis
commented
6 years ago So what's the best procedure? With step 1?
kokyriakidis
commented
6 years ago Ok this is the kmer frequency
[kyriakidk@ui3 kyriakidk]$ more freq_k32.hist
F1 31958617028
F0 3094977367
f1 2589161085
f2 182448062
f3 78785531
f4 47139273
f5 28384407
f6 21130475
f7 14353281
f8 11746673
f9 8502788
f10 7583184
f11 5869035
f12 5228492
f13 4310735
f14 3841182
f15 3372548
f16 2958430
f17 2796366
f18 2497192
f19 2220842
f20 2071655
f21 1920211
f22 1785256
f23 1641820
f24 1548139
f25 1453978
f26 1348387
f27 1287416
f28 1256055
f29 1207811
f30 1029205
f31 1052726
f32 1006082
f33 937207
f34 896512
f35 831747
f36 820010
f37 778788
f38 790625
f39 767795
f40 706938
f41 680623
f42 638476
f43 624427
f44 645331
f45 595467
f46 576271
f47 500900
f48 525466
f49 479743
f50 493656
f51 492538
f52 454246
f53 470155
f54 446223
f55 453706
f56 422592
f57 386648
f58 398407
f59 372447
f60 391344
f61 351841
f62 346001
f63 325377
f64 370122
f65 300342
f66 326872
f67 326668
f68 296638
f69 267930
f70 300329
f71 278309
f72 291972
f73 279434
f74 258838
f75 248687
f76 258123
f77 238375
f78 253063
f79 246729
f80 256107
f81 198032
f82 233786
f83 258345
f84 230144
f85 219002
f86 231547
f87 229372
f88 204536
f89 196487
f90 188297
f91 214279
f92 161232
f93 186575
f94 185336
f95 206056
f96 165476
f97 168952
f98 163766
f99 147252
f100 159844
f101 170098
f102 142040
f103 161975
f104 172162
f105 144098
f106 129856
f107 160040
f108 146310
f109 152640
f110 132910
f111 158984
f112 152538
f113 119448
f114 131152
f115 127958
f116 142488
f117 126822
f118 119713
f119 148786
f120 110203
f121 131263
f122 133157
f123 117599
f124 141562
f125 132026
f126 115533
f127 122940
f128 114598
f129 120890
f130 131194
f131 98992
f132 124142
f133 108392
f134 124064
f135 110463
f136 95049
f137 119020
f138 113630
f139 92958
f140 130435
f141 108349
f142 100252
f143 107586
f144 96134
f145 100383
f146 113814
f147 112652
f148 87800
f149 82854
f150 105700
f151 99282
f152 101402
f153 82743
f154 102594
f155 82743
f156 83957
f157 80850
f158 73634
f159 81992
f160 81920
f161 87097
f162 90155
f163 81838
f164 79842
f165 100577
f166 69317
f167 80990
f168 79862
f169 66408
f170 67571
f171 62393
f172 76943
f173 95453
f174 90094
f175 72524
f176 79936
f177 75734
f178 76808
f179 62302
f180 65546
f181 75882
f182 69574
f183 67557
f184 80005
f185 70570
f186 71687
f187 64431
f188 72785
f189 64427
f190 74858
f191 56124
f192 57331
f193 78043
f194 55068
f195 66664
f196 57246
f197 62509
f198 64537
f199 81085
f200 65394The command was:
./ntCard/ntcard -k32 -t10 /mnt/denovo_a/home/kyriakidk/FASTQ_FILES/ERR522068_1.fastq.gz /mnt/denovo_a/home/kyriakidk/FASTQ_FILES/ERR522068_2.fastq.gzHow do I interpret it?
kmnip
commented
6 years ago @kokyriakidis Trans-ABySS does not use the Bloom filter de bruijn graph. So, running ntCard would not help with your memory issue at all. Please recompile ABySS with a smaller max kmer size as I had suggest earlier. Thank you.
sjackman
commented
6 years ago I had asked @kokyriakidis to report the output of ntCard to predict the memory usage of ABySS.
F0 3094977367There are three billion distinct k-mers. The memory usage of ABySS is…
(8 + maxk / 4) · F₀ maxk = 512: (8 + 512 / 4) · 3e9 = 408 GB of RAM maxk = 128: (8 + 128 / 4) · 3e9 = 120 GB of RAM maxk = 32: (8 + 32 / 4) · 3e9 = 48 GB of RAM
@benvvalk I added an entry to ABySS's FAQ: https://github.com/bcgsc/abyss/wiki/ABySS-Users-FAQ#6-how-much-memory-does-abyss-use
kokyriakidis
commented
6 years ago Here is the situation. Abyss is installed in my university's cluster. I compiled it again locally in my given partition, with default maxk (128), so according to the output of ntCards I need 120gb of RAM. The job is gonna run on a 300gb RAM machine. How can I specify transabyss to use the locally compiled abyss and not just randomly try to find it and maybe use the abyss version installed in the cluster?
sjackman
commented
6 years ago @kmnip ? My guess is that it uses the version of ABySS found first in the PATH environment variable.
kmnip
commented
6 years ago Yes, it is just that simple!
For example:
ABYSS_PATH=/path/to/my/abyss/bin/directory/
export PATH=${ABYSS_PATH}:${PATH}
transabyss -k 32 --se read_1.fq read_2.fq ...On Wed, Oct 3, 2018 at 11:09 AM Shaun Jackman notifications@github.com wrote:
@kmnip https://github.com/kmnip ? My guess is that it uses the version of ABySS found first in the PATH environment variable.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bcgsc/transabyss/issues/11#issuecomment-426739363, or mute the thread https://github.com/notifications/unsubscribe-auth/AFJULmnZmToBIovTqzOdJAiQ9lNWebmvks5uhP1wgaJpZM4XEhyJ .
kokyriakidis
commented
6 years ago Hi, after running transabyss through the local compiled abyss it produced some output files but it shows up an error at the end
make: *** No rule to make target `k32.fastq.gz-1.adj'. Stop.
What is that and how can I fix it?
kmnip
commented
6 years ago Can you please report the exact command that you use and your entire log file?
On Fri, Oct 5, 2018 at 7:39 AM kokyriakidis notifications@github.com wrote:
Hi, after running transabyss through the local compiled abyss it produced some output files but it shows up an error at the end
make: *** No rule to make target `k32.fastq.gz-1.adj'. Stop.
What is that and how can I fix it?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bcgsc/transabyss/issues/11#issuecomment-427388734, or mute the thread https://github.com/notifications/unsubscribe-auth/AFJULrCcdTYwOqOpfqDn8XIBakV8h2ZIks5uh28vgaJpZM4XEhyJ .
kokyriakidis
commented
6 years ago Ok this is the command:
#!/bin/bash
#PBS -N Trans_Abyss
#PBS -q see
#PBS -j oe
#PBS -l nodes=1:ppn=32,walltime=100:00:00,mem=300gb
cd /mnt/denovo_a/groups/denovo
module load gcc openmpi/3.0.0
module load bio transabyss
export PATH=/mnt/denovo_a/groups/denovo/abyss/bin:$PATH
which ABYSS > abyss-path
k=32
transabyss --kmer $k --pe Preproccesing/ERR522068/ERR522068_1.fastq.gz Preproccesing/ERR522068/ERR522068_2.fastq.gz --outdir TransAssembly --name k$k.fastq.gz --threads=$PBS_NP &>> $PBS_JOBID.log
These are the output files:
-rw-rw-r-- 1 alcharal denovo 472602 Oct 4 21:07 coverage.hist
-rw-rw-r-- 1 alcharal denovo 1243665118 Oct 4 22:05 k32.fastq.gz-1.fa
-rw-rw-r-- 1 alcharal denovo 31253149 Oct 4 22:05 k32.fastq.gz-bubbles.fa
This is the log:
[kyriakidk@ui3 denovo]$ more TransAssembly-4843650.log
Trans-ABySS 1.5.5
CMD: /mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/transabyss-1.5.5-ujejanmbbiulwcbnju4rbmxsl2ftzwtn/transabyss --kmer 32 --pe Preproccesing/ERR522068/ERR522068_1.fastq.gz Preproccesing/ERR522068/ERR522068_2.fastq.gz --outdir T
ransAssembly --name k32.fastq.gz --threads=32
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Found Trans-ABySS directory at: /mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/transabyss-1.5.5-ujejanmbbiulwcbnju4rbmxsl2ftzwtn
Found Trans-ABySS `bin` directory at: /mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/transabyss-1.5.5-ujejanmbbiulwcbnju4rbmxsl2ftzwtn/bin
Found script at: /mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/transabyss-1.5.5-ujejanmbbiulwcbnju4rbmxsl2ftzwtn/bin/skip_psl_self.awk
Found script at: /mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/transabyss-1.5.5-ujejanmbbiulwcbnju4rbmxsl2ftzwtn/bin/skip_psl_self_ss.awk
Found `blat' at /mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/blat-35-kmoqjiuf63tcpurhp7ux4mejx45kjcf5/bin/blat
Found `MergeContigs' at /mnt/denovo_a/groups/denovo/abyss/bin/MergeContigs
Found `abyss-filtergraph' at /mnt/denovo_a/groups/denovo/abyss/bin/abyss-filtergraph
Found `abyss-map' at /mnt/denovo_a/groups/denovo/abyss/bin/abyss-map
Found `abyss-pe' at /mnt/denovo_a/groups/denovo/abyss/bin/abyss-pe
Found `abyss-junction' at /mnt/denovo_a/groups/denovo/abyss/bin/abyss-junction
# CPU(s) available: 64
# thread(s) requested: 32
# thread(s) to use: 32
CMD: bash -euo pipefail -c 'abyss-pe --directory=/mnt/denovo_a/groups/denovo/TransAssembly k=32 name=k32.fastq.gz E=0 e=2 c=2 j=32 k32.fastq.gz-1.fa k32.fastq.gz-1.adj q=3 se="/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068
_1.fastq.gz /mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_2.fastq.gz"'
make: Entering directory `/mnt/denovo_a/groups/denovo/TransAssembly'
/mnt/grsoftfs3/spaghetti/linux-centos6-x86_64/gcc-7.2.0/openmpi-3.0.0-2bh5baegnqoj5owr57j5suw5mdjvm4w3/bin/mpirun -np 32 ABYSS-P -k32 -q3 -e2 -E0 -c2 --coverage-hist=coverage.hist -s k32.fastq.gz-bubbles.fa -o k32.fastq.gz-1.fa /mnt
/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_1.fastq.gz /mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_2.fastq.gz
ABySS 2.1.1
ABYSS-P -k32 -q3 -e2 -E0 -c2 --coverage-hist=coverage.hist -s k32.fastq.gz-bubbles.fa -o k32.fastq.gz-1.fa /mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_1.fastq.gz /mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR52
2068_2.fastq.gz
Running on 32 processors
0: Running on host wn019.grid.auth.gr
1: Running on host wn019.grid.auth.gr
2: Running on host wn019.grid.auth.gr
3: Running on host wn019.grid.auth.gr
4: Running on host wn019.grid.auth.gr
5: Running on host wn019.grid.auth.gr
6: Running on host wn019.grid.auth.gr
7: Running on host wn019.grid.auth.gr
8: Running on host wn019.grid.auth.gr
9: Running on host wn019.grid.auth.gr
10: Running on host wn019.grid.auth.gr
11: Running on host wn019.grid.auth.gr
12: Running on host wn019.grid.auth.gr
13: Running on host wn019.grid.auth.gr
14: Running on host wn019.grid.auth.gr
15: Running on host wn019.grid.auth.gr
16: Running on host wn019.grid.auth.gr
17: Running on host wn019.grid.auth.gr
18: Running on host wn019.grid.auth.gr
19: Running on host wn019.grid.auth.gr
20: Running on host wn019.grid.auth.gr
21: Running on host wn019.grid.auth.gr
22: Running on host wn019.grid.auth.gr
23: Running on host wn019.grid.auth.gr
24: Running on host wn019.grid.auth.gr
25: Running on host wn019.grid.auth.gr
26: Running on host wn019.grid.auth.gr
27: Running on host wn019.grid.auth.gr
28: Running on host wn019.grid.auth.gr
29: Running on host wn019.grid.auth.gr
30: Running on host wn019.grid.auth.gr
31: Running on host wn019.grid.auth.gr
0: Reading `/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_1.fastq.gz'...
1: Reading `/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_2.fastq.gz'...
`/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_1.fastq.gz': discarded 981808 reads shorter than 32 bases
`/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_1.fastq.gz': discarded 534724 reads containing non-ACGT characters
`/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_2.fastq.gz': discarded 408048 reads shorter than 32 bases
`/mnt/denovo_a/groups/denovo/Preproccesing/ERR522068/ERR522068_2.fastq.gz': discarded 396654 reads containing non-ACGT characters
1: Loaded 96571679 k-mer.
31: Loaded 96441725 k-mer.
0: Loaded 96612752 k-mer.
2: Loaded 96979352 k-mer.
3: Loaded 96411339 k-mer.
4: Loaded 96514974 k-mer.
5: Loaded 96572027 k-mer.
6: Loaded 96853597 k-mer.
7: Loaded 96414562 k-mer.
8: Loaded 96653400 k-mer.
9: Loaded 96581736 k-mer.
10: Loaded 96961961 k-mer.
11: Loaded 96427811 k-mer.
12: Loaded 96563920 k-mer.
13: Loaded 96600862 k-mer.
14: Loaded 96833285 k-mer.
15: Loaded 96445045 k-mer.
16: Loaded 96603539 k-mer.
17: Loaded 96573073 k-mer.
18: Loaded 96961280 k-mer.
19: Loaded 96413494 k-mer.
20: Loaded 96545421 k-mer.
21: Loaded 96584490 k-mer.
22: Loaded 96882069 k-mer.
23: Loaded 96429768 k-mer.
24: Loaded 96643322 k-mer.
25: Loaded 96556210 k-mer.
26: Loaded 96928714 k-mer.
27: Loaded 96443751 k-mer.
28: Loaded 96577270 k-mer.
29: Loaded 96576442 k-mer.
30: Loaded 96863206 k-mer.
Loaded 3092022076 k-mer. At least 124 GB of RAM is required.
Minimum k-mer coverage is 350
Using a coverage threshold of 2...
The median k-mer coverage is 3
The reconstruction is 505212161
The k-mer coverage threshold is 1.73205
Finding adjacent k-mer...
1: Added 196314950 edges.
31: Added 196026649 edges.
30: Added 196901914 edges.
2: Added 197216564 edges.
3: Added 195954527 edges.
4: Added 196280628 edges.
5: Added 196301867 edges.
6: Added 196901722 edges.
7: Added 195945932 edges.
8: Added 196547312 edges.
9: Added 196317330 edges.
10: Added 197191114 edges.
11: Added 195976674 edges.
12: Added 196338786 edges.
13: Added 196384374 edges.
14: Added 196849047 edges.
15: Added 196043294 edges.
16: Added 196424160 edges.
17: Added 196318096 edges.
18: Added 197185879 edges.
19: Added 195953139 edges.
20: Added 196346892 edges.
21: Added 196330028 edges.
22: Added 196977454 edges.
23: Added 195975453 edges.
24: Added 196544172 edges.
25: Added 196283212 edges.
26: Added 197117228 edges.
27: Added 196010697 edges.
28: Added 196391378 edges.
29: Added 196326593 edges.
0: Added 196434369 edges.
Added 6286111434 edges.
Eroding tips...
29: Eroded 62286840 tips.
25: Eroded 62325298 tips.
5: Eroded 62364282 tips.
14: Eroded 62516162 tips.
7: Eroded 63942359 tips.
12: Eroded 64327248 tips.
17: Eroded 64806353 tips.
0: Eroded 64899218 tips.
8: Eroded 64987169 tips.
27: Eroded 64961802 tips.
9: Eroded 65241144 tips.
19: Eroded 65156614 tips.
31: Eroded 65235982 tips.
20: Eroded 65371000 tips.
24: Eroded 65452445 tips.
1: Eroded 65527132 tips.
28: Eroded 65488928 tips.
3: Eroded 65435805 tips.
23: Eroded 65474177 tips.
2: Eroded 65834786 tips.
4: Eroded 65529914 tips.
30: Eroded 65840219 tips.
21: Eroded 65695613 tips.
10: Eroded 65998870 tips.
16: Eroded 65767007 tips.
22: Eroded 65970469 tips.
15: Eroded 65719863 tips.
6: Eroded 66016040 tips.
18: Eroded 66079279 tips.
11: Eroded 65776882 tips.
26: Eroded 66066845 tips.
13: Eroded 65939582 tips.
17: Eroded 1167763 tips.
24: Eroded 489271 tips.
19: Eroded 695876 tips.
4: Eroded 336449 tips.
23: Eroded 388819 tips.
28: Eroded 428698 tips.
2: Eroded 347731 tips.
25: Eroded 3617746 tips.
15: Eroded 147675 tips.
14: Eroded 3596486 tips.
0: Eroded 1028211 tips.
Eroded 2111142601 tips.
27: Eroded 918341 tips.
21: Eroded 267179 tips.
18: Eroded 92350 tips.
7: Eroded 1921660 tips.
26: Eroded 86928 tips.
5: Eroded 3591720 tips.
22: Eroded 161469 tips.
10: Eroded 179251 tips.
12: Eroded 1584538 tips.
6: Eroded 110064 tips.
9: Eroded 727461 tips.
31: Eroded 623006 tips.
30: Eroded 297577 tips.
16: Eroded 172224 tips.
3: Eroded 426653 tips.
20: Eroded 514495 tips.
29: Eroded 3664728 tips.
11: Eroded 89485 tips.
8: Eroded 969839 tips.
1: Eroded 437833 tips.
13: Eroded 25748 tips.
Pruning tips shorter than 1 bp...
5: Pruned 61009 tips.
14: Pruned 60783 tips.
25: Pruned 60801 tips.
12: Pruned 60550 tips.
29: Pruned 60937 tips.
0: Pruned 60436 tips.
7: Pruned 60067 tips.
31: Pruned 60334 tips.
17: Pruned 60831 tips.
1: Pruned 60321 tips.
20: Pruned 60660 tips.
8: Pruned 61148 tips.
27: Pruned 60583 tips.
3: Pruned 60234 tips.
6: Pruned 61034 tips.
30: Pruned 60863 tips.
11: Pruned 60365 tips.
15: Pruned 60406 tips.
21: Pruned 60748 tips.
26: Pruned 60985 tips.
22: Pruned 60249 tips.
9: Pruned 60946 tips.
4: Pruned 60776 tips.
28: Pruned 61315 tips.
13: Pruned 61149 tips.
10: Pruned 61334 tips.
19: Pruned 60549 tips.
23: Pruned 59835 tips.
18: Pruned 61040 tips.
2: Pruned 61105 tips.
24: Pruned 60820 tips.
16: Pruned 60664 tips.
Pruned 1942877 k-mer in 1942877 tips.
Pruning tips shorter than 2 bp...
5: Pruned 21777 tips.
25: Pruned 21742 tips.
14: Pruned 21952 tips.
12: Pruned 21949 tips.
29: Pruned 22029 tips.
0: Pruned 21445 tips.
31: Pruned 21921 tips.
7: Pruned 21550 tips.
20: Pruned 21997 tips.
17: Pruned 21716 tips.
8: Pruned 21437 tips.
27: Pruned 21581 tips.
1: Pruned 21954 tips.
28: Pruned 21804 tips.
30: Pruned 21924 tips.
15: Pruned 21620 tips.
23: Pruned 21288 tips.
6: Pruned 22033 tips.
4: Pruned 21256 tips.
11: Pruned 21559 tips.
19: Pruned 21647 tips.
3: Pruned 21661 tips.
21: Pruned 21760 tips.
9: Pruned 21750 tips.
13: Pruned 21666 tips.
26: Pruned 21994 tips.
22: Pruned 22042 tips.
10: Pruned 22110 tips.
16: Pruned 21922 tips.
2: Pruned 22142 tips.
18: Pruned 21627 tips.
24: Pruned 21555 tips.
Pruned 1359017 k-mer in 696410 tips.
Pruning tips shorter than 4 bp...
25: Pruned 24552 tips.
5: Pruned 24495 tips.
14: Pruned 24284 tips.
12: Pruned 24357 tips.
29: Pruned 24383 tips.
0: Pruned 24315 tips.
20: Pruned 24158 tips.
31: Pruned 24318 tips.
6: Pruned 24223 tips.
27: Pruned 24221 tips.
7: Pruned 24077 tips.
3: Pruned 24142 tips.
17: Pruned 24561 tips.
1: Pruned 24244 tips.
8: Pruned 24199 tips.
23: Pruned 24050 tips.
28: Pruned 24262 tips.
30: Pruned 24290 tips.
15: Pruned 23672 tips.
4: Pruned 24141 tips.
21: Pruned 24452 tips.
13: Pruned 24432 tips.
19: Pruned 24483 tips.
10: Pruned 24382 tips.
22: Pruned 24391 tips.
9: Pruned 24249 tips.
26: Pruned 24642 tips.
16: Pruned 24111 tips.
18: Pruned 24369 tips.
2: Pruned 24194 tips.
24: Pruned 24357 tips.
11: Pruned 24111 tips.
Pruned 2605800 k-mer in 777117 tips.
Pruning tips shorter than 8 bp...
25: Pruned 24674 tips.
14: Pruned 24383 tips.
5: Pruned 24722 tips.
12: Pruned 24287 tips.
29: Pruned 24697 tips.
20: Pruned 24507 tips.
6: Pruned 24657 tips.
0: Pruned 24908 tips.
28: Pruned 24682 tips.
27: Pruned 24440 tips.
3: Pruned 24530 tips.
7: Pruned 24236 tips.
8: Pruned 24283 tips.
31: Pruned 24404 tips.
1: Pruned 24622 tips.
23: Pruned 24410 tips.
4: Pruned 24527 tips.
11: Pruned 24502 tips.
15: Pruned 24136 tips.
30: Pruned 24460 tips.
19: Pruned 24292 tips.
21: Pruned 24284 tips.
17: Pruned 24798 tips.
22: Pruned 24618 tips.
13: Pruned 24565 tips.
10: Pruned 24742 tips.
26: Pruned 24721 tips.
9: Pruned 24318 tips.
18: Pruned 24930 tips.
16: Pruned 24585 tips.
2: Pruned 24730 tips.
24: Pruned 24520 tips.
Pruned 4700541 k-mer in 785170 tips.
Pruning tips shorter than 16 bp...
5: Pruned 24775 tips.
14: Pruned 24727 tips.
12: Pruned 24655 tips.
25: Pruned 24399 tips.
29: Pruned 24568 tips.
20: Pruned 24464 tips.
6: Pruned 24805 tips.
30: Pruned 24555 tips.
7: Pruned 24423 tips.
28: Pruned 24426 tips.
31: Pruned 24410 tips.
23: Pruned 24354 tips.
4: Pruned 24168 tips.
15: Pruned 24163 tips.
21: Pruned 24508 tips.
27: Pruned 24276 tips.
13: Pruned 24922 tips.
0: Pruned 24366 tips.
22: Pruned 24585 tips.
3: Pruned 24269 tips.
8: Pruned 24442 tips.
17: Pruned 24128 tips.
1: Pruned 24301 tips.
19: Pruned 24415 tips.
26: Pruned 24614 tips.
10: Pruned 24406 tips.
11: Pruned 24303 tips.
9: Pruned 24418 tips.
16: Pruned 24510 tips.
18: Pruned 24757 tips.
2: Pruned 24610 tips.
24: Pruned 24577 tips.
Pruned 9198680 k-mer in 783299 tips.
Pruning tips shorter than 32 bp...
25: Pruned 19034 tips.
5: Pruned 18797 tips.
14: Pruned 18822 tips.
12: Pruned 18357 tips.
29: Pruned 18593 tips.
20: Pruned 18644 tips.
6: Pruned 18899 tips.
27: Pruned 18622 tips.
30: Pruned 18942 tips.
0: Pruned 18941 tips.
28: Pruned 18948 tips.
8: Pruned 18908 tips.
3: Pruned 18736 tips.
1: Pruned 18535 tips.
7: Pruned 18627 tips.
31: Pruned 18719 tips.
17: Pruned 18932 tips.
23: Pruned 18832 tips.
4: Pruned 18919 tips.
15: Pruned 18564 tips.
21: Pruned 18816 tips.
13: Pruned 18709 tips.
22: Pruned 18826 tips.
19: Pruned 18585 tips.
18: Pruned 18963 tips.
26: Pruned 18828 tips.
11: Pruned 18584 tips.
10: Pruned 18887 tips.
9: Pruned 18662 tips.
24: Pruned 18767 tips.
2: Pruned 18765 tips.
16: Pruned 19012 tips.
Pruned 12694933 k-mer in 600775 tips.
Pruning tips shorter than 32 bp...
25: Pruned 93 tips.
5: Pruned 85 tips.
14: Pruned 80 tips.
12: Pruned 79 tips.
29: Pruned 96 tips.
6: Pruned 89 tips.
28: Pruned 72 tips.
20: Pruned 86 tips.
30: Pruned 91 tips.
27: Pruned 89 tips.
3: Pruned 80 tips.
8: Pruned 100 tips.
17: Pruned 79 tips.
31: Pruned 92 tips.
0: Pruned 70 tips.
7: Pruned 68 tips.
1: Pruned 84 tips.
23: Pruned 86 tips.
4: Pruned 78 tips.
11: Pruned 77 tips.
21: Pruned 79 tips.
22: Pruned 91 tips.
19: Pruned 76 tips.
13: Pruned 74 tips.
18: Pruned 87 tips.
26: Pruned 75 tips.
15: Pruned 74 tips.
10: Pruned 67 tips.
16: Pruned 80 tips.
9: Pruned 94 tips.
2: Pruned 82 tips.
24: Pruned 88 tips.
Pruned 22639 k-mer in 2641 tips.
Pruning tips shorter than 32 bp...
25: Pruned 0 tips.
12: Pruned 0 tips.
5: Pruned 1 tips.
14: Pruned 2 tips.
29: Pruned 1 tips.
28: Pruned 2 tips.
20: Pruned 0 tips.
8: Pruned 1 tips.
0: Pruned 1 tips.
1: Pruned 0 tips.
17: Pruned 0 tips.
4: Pruned 0 tips.
6: Pruned 0 tips.
21: Pruned 0 tips.
13: Pruned 0 tips.
30: Pruned 0 tips.
7: Pruned 0 tips.
31: Pruned 0 tips.
23: Pruned 0 tips.
9: Pruned 0 tips.
24: Pruned 0 tips.
15: Pruned 2 tips.
16: Pruned 0 tips.
22: Pruned 0 tips.
27: Pruned 0 tips.
3: Pruned 1 tips.
19: Pruned 1 tips.
10: Pruned 2 tips.
11: Pruned 2 tips.
26: Pruned 1 tips.
2: Pruned 0 tips.
18: Pruned 0 tips.
Pruned 169 k-mer in 17 tips.
Pruning tips shorter than 32 bp...
25: Pruned 0 tips.
14: Pruned 0 tips.
5: Pruned 0 tips.
12: Pruned 0 tips.
29: Pruned 0 tips.
6: Pruned 0 tips.
20: Pruned 0 tips.
28: Pruned 0 tips.
8: Pruned 0 tips.
27: Pruned 0 tips.
0: Pruned 0 tips.
31: Pruned 0 tips.
1: Pruned 0 tips.
30: Pruned 0 tips.
17: Pruned 0 tips.
4: Pruned 0 tips.
23: Pruned 0 tips.
22: Pruned 0 tips.
15: Pruned 0 tips.
13: Pruned 0 tips.
21: Pruned 0 tips.
7: Pruned 0 tips.
19: Pruned 0 tips.
3: Pruned 0 tips.
26: Pruned 0 tips.
9: Pruned 0 tips.
11: Pruned 0 tips.
24: Pruned 0 tips.
18: Pruned 0 tips.
10: Pruned 0 tips.
2: Pruned 0 tips.
16: Pruned 0 tips.
Pruned 5588306 tips in 8 rounds.
Marking ambiguous branches...
25: Marked 5728998 edges of 2365951 ambiguous vertices.
29: Marked 5737880 edges of 2368545 ambiguous vertices.
7: Marked 5662416 edges of 2338965 ambiguous vertices.
14: Marked 5747177 edges of 2375643 ambiguous vertices.
5: Marked 5720392 edges of 2363771 ambiguous vertices.
19: Marked 5670606 edges of 2341015 ambiguous vertices.
31: Marked 5695216 edges of 2350049 ambiguous vertices.
27: Marked 5677126 edges of 2346060 ambiguous vertices.
9: Marked 5714807 edges of 2362250 ambiguous vertices.
12: Marked 5783007 edges of 2385943 ambiguous vertices.
30: Marked 5741801 edges of 2373913 ambiguous vertices.
8: Marked 5819997 edges of 2401802 ambiguous vertices.
24: Marked 5843257 edges of 2408738 ambiguous vertices.
3: Marked 5679016 edges of 2344844 ambiguous vertices.
17: Marked 5741046 edges of 2370072 ambiguous vertices.
6: Marked 5762834 edges of 2381614 ambiguous vertices.
28: Marked 5822124 edges of 2398610 ambiguous vertices.
15: Marked 5700809 edges of 2352294 ambiguous vertices.
23: Marked 5665974 edges of 2339979 ambiguous vertices.
1: Marked 5739927 edges of 2371444 ambiguous vertices.
21: Marked 5721571 edges of 2365096 ambiguous vertices.
20: Marked 5846689 edges of 2405370 ambiguous vertices.
0: Marked 5798437 edges of 2410729 ambiguous vertices.
22: Marked 5783069 edges of 2388992 ambiguous vertices.
11: Marked 5663313 edges of 2340170 ambiguous vertices.
26: Marked 5843283 edges of 2412610 ambiguous vertices.
10: Marked 5859239 edges of 2418223 ambiguous vertices.
2: Marked 5848004 edges of 2412309 ambiguous vertices.
18: Marked 5850423 edges of 2413962 ambiguous vertices.
4: Marked 5842364 edges of 2402072 ambiguous vertices.
16: Marked 5786906 edges of 2387382 ambiguous vertices.
13: Marked 5746010 edges of 2371531 ambiguous vertices.
Marked 76069948 ambiguous branches.
Removing low-coverage contigs (mean k-mer coverage < 2)...
25: Found 29549561 k-mer in 2316206 contigs before removing low-coverage contigs.
Removed 16466771 k-mer in 802777 low-coverage contigs.
14: Found 29760987 k-mer in 2329651 contigs before removing low-coverage contigs.
Removed 16583341 k-mer in 808962 low-coverage contigs.
5: Found 29596815 k-mer in 2312802 contigs before removing low-coverage contigs.
Removed 16473764 k-mer in 801163 low-coverage contigs.
12: Found 29638548 k-mer in 2327225 contigs before removing low-coverage contigs.
Removed 16516620 k-mer in 806870 low-coverage contigs.
29: Found 29631675 k-mer in 2320369 contigs before removing low-coverage contigs.
Removed 16487062 k-mer in 804715 low-coverage contigs.
30: Found 29719056 k-mer in 2328061 contigs before removing low-coverage contigs.
Removed 16551278 k-mer in 808028 low-coverage contigs.
28: Found 29665751 k-mer in 2335858 contigs before removing low-coverage contigs.
Removed 16508730 k-mer in 809784 low-coverage contigs.
27: Found 29516115 k-mer in 2301706 contigs before removing low-coverage contigs.
Removed 16433280 k-mer in 796538 low-coverage contigs.
0: Found 29641831 k-mer in 2341389 contigs before removing low-coverage contigs.
Removed 16516705 k-mer in 813457 low-coverage contigs.
24: Found 29647825 k-mer in 2339532 contigs before removing low-coverage contigs.
Removed 16519314 k-mer in 810487 low-coverage contigs.
20: Found 29683470 k-mer in 2339376 contigs before removing low-coverage contigs.
Removed 16499990 k-mer in 808731 low-coverage contigs.
6: Found 29703248 k-mer in 2334306 contigs before removing low-coverage contigs.
Removed 16575601 k-mer in 810940 low-coverage contigs.
8: Found 29725502 k-mer in 2339085 contigs before removing low-coverage contigs.
Removed 16547419 k-mer in 811946 low-coverage contigs.
3: Found 29467201 k-mer in 2299336 contigs before removing low-coverage contigs.
Removed 16402470 k-mer in 797189 low-coverage contigs.
31: Found 29538269 k-mer in 2305490 contigs before removing low-coverage contigs.
Removed 16430007 k-mer in 798043 low-coverage contigs.
23: Found 29527381 k-mer in 2297635 contigs before removing low-coverage contigs.
Removed 16357045 k-mer in 793460 low-coverage contigs.
4: Found 29542995 k-mer in 2331197 contigs before removing low-coverage contigs.
Removed 16416456 k-mer in 804974 low-coverage contigs.
11: Found 29421192 k-mer in 2295437 contigs before removing low-coverage contigs.
Removed 16392230 k-mer in 794957 low-coverage contigs.
1: Found 29587520 k-mer in 2316415 contigs before removing low-coverage contigs.
Removed 16474355 k-mer in 803943 low-coverage contigs.
7: Found 29482104 k-mer in 2298051 contigs before removing low-coverage contigs.
Removed 16394791 k-mer in 795226 low-coverage contigs.
15: Found 29599308 k-mer in 2307761 contigs before removing low-coverage contigs.
Removed 16502364 k-mer in 800004 low-coverage contigs.
21: Found 29628821 k-mer in 2316013 contigs before removing low-coverage contigs.
Removed 16510810 k-mer in 803835 low-coverage contigs.
26: Found 29776572 k-mer in 2353456 contigs before removing low-coverage contigs.
Removed 16590655 k-mer in 816927 low-coverage contigs.
17: Found 29515979 k-mer in 2317486 contigs before removing low-coverage contigs.
Removed 16432970 k-mer in 803639 low-coverage contigs.
13: Found 29659773 k-mer in 2323940 contigs before removing low-coverage contigs.
Removed 16503702 k-mer in 805852 low-coverage contigs.
22: Found 29801805 k-mer in 2343654 contigs before removing low-coverage contigs.
Removed 16625477 k-mer in 814581 low-coverage contigs.
9: Found 29614122 k-mer in 2315395 contigs before removing low-coverage contigs.
Removed 16464854 k-mer in 802080 low-coverage contigs.
19: Found 29476914 k-mer in 2299333 contigs before removing low-coverage contigs.
Removed 16414595 k-mer in 797379 low-coverage contigs.
10: Found 29866884 k-mer in 2358619 contigs before removing low-coverage contigs.
Removed 16650847 k-mer in 820205 low-coverage contigs.
2: Found 29807291 k-mer in 2355286 contigs before removing low-coverage contigs.
Removed 16617930 k-mer in 817830 low-coverage contigs.
16: Found 29615344 k-mer in 2327408 contigs before removing low-coverage contigs.
Removed 16472144 k-mer in 805866 low-coverage contigs.
Found 948264702 k-mer in 74381449 contigs before removing low-coverage contigs.
Removed 527960963 k-mer in 25787359 low-coverage contigs.
Splitting ambiguous branches...
18: Found 29854843 k-mer in 2353971 contigs before removing low-coverage contigs.
Removed 16627386 k-mer in 816971 low-coverage contigs.
25: Split 1596646 ambigiuous branches.
29: Split 1597827 ambigiuous branches.
14: Split 1605251 ambigiuous branches.
7: Split 1580848 ambigiuous branches.
5: Split 1593735 ambigiuous branches.
31: Split 1583674 ambigiuous branches.
12: Split 1604639 ambigiuous branches.
27: Split 1585019 ambigiuous branches.
9: Split 1596349 ambigiuous branches.
24: Split 1617189 ambigiuous branches.
8: Split 1615367 ambigiuous branches.
23: Split 1580359 ambigiuous branches.
17: Split 1599092 ambigiuous branches.
30: Split 1606326 ambigiuous branches.
19: Split 1582162 ambigiuous branches.
11: Split 1582162 ambigiuous branches.
2: Split 1628611 ambigiuous branches.
0: Split 1618064 ambigiuous branches.
28: Split 1609005 ambigiuous branches.
6: Split 1610583 ambigiuous branches.
3: Split 1582843 ambigiuous branches.
20: Split 1609406 ambigiuous branches.
21: Split 1597084 ambigiuous branches.
1: Split 1601651 ambigiuous branches.
26: Split 1623172 ambigiuous branches.
22: Split 1617395 ambigiuous branches.
4: Split 1605009 ambigiuous branches.
15: Split 1586189 ambigiuous branches.
18: Split 1624564 ambigiuous branches.
10: Split 1629125 ambigiuous branches.
16: Split 1606388 ambigiuous branches.
13: Split 1600082 ambigiuous branches.
Split 51275816 ambiguous branches.
Removed 527960963 marked k-mer.
Eroding tips...
25: Eroded 5437 tips.
31: Eroded 5372 tips.
27: Eroded 5565 tips.
24: Eroded 5642 tips.
29: Eroded 5735 tips.
2: Eroded 5886 tips.
5: Eroded 5927 tips.
21: Eroded 7628 tips.
19: Eroded 7645 tips.
8: Eroded 7767 tips.
17: Eroded 7740 tips.
23: Eroded 7806 tips.
28: Eroded 7860 tips.
30: Eroded 7974 tips.
20: Eroded 7858 tips.
9: Eroded 8188 tips.
10: Eroded 8034 tips.
15: Eroded 7954 tips.
7: Eroded 8102 tips.
16: Eroded 8207 tips.
0: Eroded 8097 tips.
6: Eroded 8203 tips.
26: Eroded 8438 tips.
12: Eroded 8248 tips.
18: Eroded 8472 tips.
13: Eroded 8503 tips.
3: Eroded 8366 tips.
11: Eroded 8783 tips.
14: Eroded 9347 tips.
1: Eroded 9132 tips.
4: Eroded 9050 tips.
22: Eroded 9258 tips.
14: Eroded 4884 tips.
7: Eroded 5864 tips.
3: Eroded 5365 tips.
20: Eroded 6134 tips.
4: Eroded 4790 tips.
28: Eroded 6235 tips.
16: Eroded 5775 tips.
30: Eroded 6195 tips.
13: Eroded 5525 tips.
15: Eroded 6075 tips.
12: Eroded 5699 tips.
19: Eroded 6294 tips.
18: Eroded 5764 tips.
9: Eroded 5916 tips.
23: Eroded 6073 tips.
6: Eroded 5987 tips.
24: Eroded 8458 tips.
10: Eroded 6086 tips.
11: Eroded 5149 tips.
27: Eroded 8527 tips.
0: Eroded 5878 tips.
Eroded 449312 tips.
17: Eroded 6437 tips.
26: Eroded 5794 tips.
1: Eroded 4991 tips.
8: Eroded 6343 tips.
29: Eroded 8539 tips.
25: Eroded 8593 tips.
5: Eroded 8126 tips.
21: Eroded 6238 tips.
31: Eroded 8434 tips.
2: Eroded 8132 tips.
22: Eroded 4788 tips.
Pruning tips shorter than 1 bp...
5: Pruned 35509 tips.
25: Pruned 35429 tips.
14: Pruned 35678 tips.
12: Pruned 35798 tips.
29: Pruned 35830 tips.
0: Pruned 35702 tips.
7: Pruned 35064 tips.
3: Pruned 34828 tips.
27: Pruned 35011 tips.
23: Pruned 34892 tips.
8: Pruned 36249 tips.
15: Pruned 34872 tips.
4: Pruned 35578 tips.
31: Pruned 35150 tips.
30: Pruned 35921 tips.
17: Pruned 35803 tips.
28: Pruned 36034 tips.
19: Pruned 34894 tips.
6: Pruned 36084 tips.
20: Pruned 35993 tips.
21: Pruned 35384 tips.
13: Pruned 36084 tips.
1: Pruned 35574 tips.
26: Pruned 36497 tips.
9: Pruned 35603 tips.
11: Pruned 35256 tips.
22: Pruned 36008 tips.
10: Pruned 36902 tips.
2: Pruned 36405 tips.
18: Pruned 36424 tips.
16: Pruned 35879 tips.
24: Pruned 35952 tips.
Pruned 1142287 k-mer in 1142287 tips.
Pruning tips shorter than 2 bp...
25: Pruned 24717 tips.
5: Pruned 24424 tips.
14: Pruned 24551 tips.
12: Pruned 24600 tips.
29: Pruned 24258 tips.
7: Pruned 23760 tips.
0: Pruned 24262 tips.
27: Pruned 23928 tips.
3: Pruned 24082 tips.
8: Pruned 24308 tips.
28: Pruned 24353 tips.
6: Pruned 24694 tips.
30: Pruned 24603 tips.
20: Pruned 24228 tips.
15: Pruned 23912 tips.
31: Pruned 23946 tips.
23: Pruned 23826 tips.
17: Pruned 24722 tips.
11: Pruned 24224 tips.
21: Pruned 24376 tips.
4: Pruned 24452 tips.
13: Pruned 24374 tips.
1: Pruned 24462 tips.
9: Pruned 24644 tips.
10: Pruned 24863 tips.
26: Pruned 24908 tips.
22: Pruned 24831 tips.
19: Pruned 24107 tips.
2: Pruned 24883 tips.
18: Pruned 24879 tips.
16: Pruned 24533 tips.
24: Pruned 24512 tips.
Pruned 1185774 k-mer in 781222 tips.
Pruning tips shorter than 4 bp...
25: Pruned 31388 tips.
5: Pruned 31139 tips.
12: Pruned 31269 tips.
14: Pruned 31315 tips.
29: Pruned 31124 tips.
28: Pruned 31359 tips.
27: Pruned 30809 tips.
6: Pruned 31726 tips.
3: Pruned 30741 tips.
7: Pruned 31060 tips.
30: Pruned 31467 tips.
0: Pruned 30993 tips.
8: Pruned 31385 tips.
17: Pruned 31333 tips.
20: Pruned 30876 tips.
23: Pruned 30867 tips.
31: Pruned 30878 tips.
1: Pruned 31395 tips.
4: Pruned 30830 tips.
19: Pruned 30902 tips.
11: Pruned 30776 tips.
15: Pruned 31001 tips.
13: Pruned 31446 tips.
26: Pruned 31678 tips.
21: Pruned 31336 tips.
10: Pruned 31585 tips.
9: Pruned 31301 tips.
22: Pruned 31834 tips.
18: Pruned 31451 tips.
2: Pruned 31989 tips.
16: Pruned 31523 tips.
24: Pruned 31357 tips.
Pruned 2589935 k-mer in 1000133 tips.
Pruning tips shorter than 8 bp...
25: Pruned 34689 tips.
5: Pruned 34634 tips.
14: Pruned 34865 tips.
12: Pruned 34147 tips.
29: Pruned 34505 tips.
27: Pruned 34787 tips.
28: Pruned 34622 tips.
3: Pruned 34145 tips.
8: Pruned 34399 tips.
6: Pruned 35101 tips.
7: Pruned 34313 tips.
30: Pruned 34805 tips.
0: Pruned 34626 tips.
23: Pruned 34274 tips.
4: Pruned 34452 tips.
17: Pruned 34499 tips.
19: Pruned 34061 tips.
20: Pruned 34546 tips.
11: Pruned 34175 tips.
31: Pruned 34304 tips.
15: Pruned 34268 tips.
13: Pruned 34463 tips.
26: Pruned 34995 tips.
21: Pruned 34867 tips.
10: Pruned 35003 tips.
22: Pruned 34598 tips.
9: Pruned 34156 tips.
24: Pruned 34252 tips.
18: Pruned 34655 tips.
2: Pruned 34635 tips.
16: Pruned 34300 tips.
1: Pruned 34377 tips.
Pruned 5262444 k-mer in 1104518 tips.
Pruning tips shorter than 16 bp...
25: Pruned 30901 tips.
5: Pruned 30588 tips.
12: Pruned 31051 tips.
14: Pruned 30829 tips.
29: Pruned 30475 tips.
8: Pruned 30757 tips.
6: Pruned 30873 tips.
27: Pruned 30870 tips.
20: Pruned 30715 tips.
30: Pruned 30841 tips.
3: Pruned 30532 tips.
28: Pruned 30725 tips.
7: Pruned 30335 tips.
23: Pruned 30559 tips.
0: Pruned 30857 tips.
4: Pruned 30572 tips.
31: Pruned 30665 tips.
17: Pruned 30442 tips.
11: Pruned 30744 tips.
1: Pruned 30571 tips.
13: Pruned 30528 tips.
21: Pruned 30782 tips.
26: Pruned 30844 tips.
15: Pruned 30536 tips.
10: Pruned 30734 tips.
22: Pruned 30885 tips.
9: Pruned 30624 tips.
18: Pruned 31338 tips.
2: Pruned 30953 tips.
19: Pruned 30621 tips.
24: Pruned 30818 tips.
16: Pruned 30842 tips.
Pruned 9544806 k-mer in 983407 tips.
Pruning tips shorter than 32 bp...
25: Pruned 18396 tips.
12: Pruned 18521 tips.
5: Pruned 18482 tips.
14: Pruned 18418 tips.
29: Pruned 18467 tips.
6: Pruned 18488 tips.
28: Pruned 18614 tips.
27: Pruned 18485 tips.
30: Pruned 18681 tips.
8: Pruned 18461 tips.
20: Pruned 18520 tips.
3: Pruned 18365 tips.
7: Pruned 18571 tips.
23: Pruned 18422 tips.
0: Pruned 18422 tips.
4: Pruned 18436 tips.
31: Pruned 18572 tips.
17: Pruned 18137 tips.
13: Pruned 18543 tips.
15: Pruned 18592 tips.
11: Pruned 18512 tips.
21: Pruned 18593 tips.
26: Pruned 18654 tips.
1: Pruned 18628 tips.
19: Pruned 18160 tips.
22: Pruned 18516 tips.
10: Pruned 18701 tips.
9: Pruned 18367 tips.
2: Pruned 18615 tips.
24: Pruned 18312 tips.
18: Pruned 18584 tips.
16: Pruned 18540 tips.
Pruned 11720264 k-mer in 591775 tips.
Pruning tips shorter than 32 bp...
25: Pruned 44 tips.
5: Pruned 61 tips.
12: Pruned 46 tips.
14: Pruned 44 tips.
29: Pruned 52 tips.
27: Pruned 36 tips.
6: Pruned 58 tips.
30: Pruned 42 tips.
28: Pruned 51 tips.
8: Pruned 38 tips.
20: Pruned 45 tips.
3: Pruned 58 tips.
23: Pruned 36 tips.
7: Pruned 44 tips.
31: Pruned 44 tips.
4: Pruned 39 tips.
0: Pruned 62 tips.
17: Pruned 48 tips.
15: Pruned 49 tips.
11: Pruned 44 tips.
13: Pruned 48 tips.
1: Pruned 42 tips.
26: Pruned 65 tips.
19: Pruned 46 tips.
21: Pruned 54 tips.
22: Pruned 47 tips.
10: Pruned 54 tips.
9: Pruned 57 tips.
18: Pruned 53 tips.
2: Pruned 54 tips.
24: Pruned 41 tips.
16: Pruned 47 tips.
Pruned 10929 k-mer in 1549 tips.
Pruning tips shorter than 32 bp...
25: Pruned 2 tips.
12: Pruned 1 tips.
5: Pruned 0 tips.
14: Pruned 0 tips.
29: Pruned 0 tips.
27: Pruned 0 tips.
28: Pruned 0 tips.
30: Pruned 0 tips.
6: Pruned 0 tips.
8: Pruned 0 tips.
20: Pruned 2 tips.
23: Pruned 0 tips.
7: Pruned 0 tips.
17: Pruned 0 tips.
4: Pruned 0 tips.
3: Pruned 0 tips.
0: Pruned 1 tips.
31: Pruned 0 tips.
1: Pruned 0 tips.
13: Pruned 1 tips.
15: Pruned 0 tips.
26: Pruned 1 tips.
11: Pruned 0 tips.
21: Pruned 0 tips.
10: Pruned 0 tips.
19: Pruned 0 tips.
22: Pruned 0 tips.
9: Pruned 0 tips.
18: Pruned 0 tips.
24: Pruned 0 tips.
16: Pruned 1 tips.
2: Pruned 0 tips.
Pruned 65 k-mer in 9 tips.
Pruning tips shorter than 32 bp...
25: Pruned 0 tips.
12: Pruned 0 tips.
14: Pruned 0 tips.
5: Pruned 0 tips.
29: Pruned 0 tips.
27: Pruned 0 tips.
8: Pruned 0 tips.
6: Pruned 0 tips.
30: Pruned 0 tips.
3: Pruned 0 tips.
20: Pruned 0 tips.
28: Pruned 0 tips.
7: Pruned 0 tips.
17: Pruned 0 tips.
23: Pruned 0 tips.
0: Pruned 0 tips.
4: Pruned 0 tips.
31: Pruned 0 tips.
11: Pruned 0 tips.
1: Pruned 0 tips.
21: Pruned 0 tips.
15: Pruned 0 tips.
13: Pruned 0 tips.
22: Pruned 0 tips.
10: Pruned 0 tips.
26: Pruned 0 tips.
18: Pruned 0 tips.
2: Pruned 0 tips.
19: Pruned 0 tips.
24: Pruned 0 tips.
16: Pruned 0 tips.
9: Pruned 0 tips.
Pruned 5604900 tips in 8 rounds.
Popping bubbles...
0: Removed 11226 bubbles.
1: Removed 10664 bubbles.
2: Removed 10384 bubbles.
3: Removed 10320 bubbles.
4: Removed 9688 bubbles.
5: Removed 9531 bubbles.
6: Removed 8982 bubbles.
7: Removed 8599 bubbles.
8: Removed 8231 bubbles.
9: Removed 7978 bubbles.
10: Removed 7577 bubbles.
11: Removed 7340 bubbles.
12: Removed 6709 bubbles.
13: Removed 6562 bubbles.
14: Removed 6230 bubbles.
15: Removed 5872 bubbles.
16: Removed 5606 bubbles.
17: Removed 5131 bubbles.
18: Removed 4842 bubbles.
19: Removed 4447 bubbles.
20: Removed 3977 bubbles.
21: Removed 3683 bubbles.
22: Removed 3436 bubbles.
23: Removed 3131 bubbles.
24: Removed 2754 bubbles.
25: Removed 2374 bubbles.
26: Removed 2037 bubbles.
27: Removed 1644 bubbles.
28: Removed 1299 bubbles.
29: Removed 964 bubbles.
30: Removed 617 bubbles.
31: Removed 284 bubbles.
Removed 182119 bubbles.
Removed 182119 bubbles.
Marking ambiguous branches...
25: Marked 1620128 edges of 621514 ambiguous vertices.
29: Marked 1625918 edges of 623304 ambiguous vertices.
7: Marked 1600558 edges of 614358 ambiguous vertices.
14: Marked 1623609 edges of 624049 ambiguous vertices.
5: Marked 1618179 edges of 620970 ambiguous vertices.
9: Marked 1605509 edges of 617804 ambiguous vertices.
27: Marked 1603836 edges of 615291 ambiguous vertices.
31: Marked 1614637 edges of 618878 ambiguous vertices.
11: Marked 1594998 edges of 612482 ambiguous vertices.
6: Marked 1627203 edges of 626377 ambiguous vertices.
30: Marked 1616568 edges of 621393 ambiguous vertices.
17: Marked 1626493 edges of 624002 ambiguous vertices.
12: Marked 1640150 edges of 629144 ambiguous vertices.
19: Marked 1603109 edges of 614847 ambiguous vertices.
3: Marked 1606959 edges of 616474 ambiguous vertices.
24: Marked 1666205 edges of 638276 ambiguous vertices.
23: Marked 1603104 edges of 615213 ambiguous vertices.
8: Marked 1653429 edges of 634416 ambiguous vertices.
28: Marked 1667332 edges of 638577 ambiguous vertices.
15: Marked 1613795 edges of 618570 ambiguous vertices.
1: Marked 1623627 edges of 623461 ambiguous vertices.
21: Marked 1615333 edges of 620495 ambiguous vertices.
2: Marked 1666394 edges of 638923 ambiguous vertices.
0: Marked 1657510 edges of 645378 ambiguous vertices.
22: Marked 1634472 edges of 627360 ambiguous vertices.
10: Marked 1666683 edges of 639477 ambiguous vertices.
26: Marked 1661227 edges of 637696 ambiguous vertices.
20: Marked 1685620 edges of 644122 ambiguous vertices.
18: Marked 1664265 edges of 638220 ambiguous vertices.
4: Marked 1689587 edges of 644245 ambiguous vertices.
16: Marked 1644744 edges of 631108 ambiguous vertices.
13: Marked 1630982 edges of 625615 ambiguous vertices.
Marked 20062039 ambiguous branches.
Assembling...
25: Assembled 11899745 k-mer in 554837 contigs.
14: Assembled 11928614 k-mer in 559893 contigs.
12: Assembled 11885905 k-mer in 560351 contigs.
5: Assembled 11923902 k-mer in 555719 contigs.
16: Assembled 11953981 k-mer in 561988 contigs.
29: Assembled 11883580 k-mer in 557793 contigs.
30: Assembled 11969543 k-mer in 557112 contigs.
31: Assembled 11988780 k-mer in 554333 contigs.
27: Assembled 11757774 k-mer in 550570 contigs.
8: Assembled 11987202 k-mer in 564164 contigs.
28: Assembled 12002382 k-mer in 566343 contigs.
11: Assembled 11800429 k-mer in 550702 contigs.
6: Assembled 11941385 k-mer in 560713 contigs.
3: Assembled 11855373 k-mer in 551706 contigs.
4: Assembled 11989821 k-mer in 568682 contigs.
0: Assembled 11922792 k-mer in 567985 contigs.
24: Assembled 11904633 k-mer in 565352 contigs.
20: Assembled 11943762 k-mer in 569997 contigs.
26: Assembled 11938503 k-mer in 568831 contigs.
21: Assembled 11906659 k-mer in 554400 contigs.
23: Assembled 11938672 k-mer in 553097 contigs.
7: Assembled 11917353 k-mer in 550609 contigs.
15: Assembled 11942314 k-mer in 553523 contigs.
1: Assembled 11978549 k-mer in 557106 contigs.
22: Assembled 11996369 k-mer in 563520 contigs.
13: Assembled 11891489 k-mer in 558501 contigs.
10: Assembled 12105875 k-mer in 570401 contigs.
17: Assembled 11869479 k-mer in 557486 contigs.
2: Assembled 12020014 k-mer in 568272 contigs.
9: Assembled 11900189 k-mer in 554719 contigs.
19: Assembled 11865181 k-mer in 550912 contigs.
18: Assembled 12008809 k-mer in 567538 contigs.
Assembled 381819058 k-mer in 17907155 contigs.
Concatenating fasta files to k32.fastq.gz-1.fa
Concatenating fasta files to k32.fastq.gz-bubbles.fa
Done.
make: *** No rule to make target `k32.fastq.gz-1.adj'. Stop.
make: Leaving directory `/mnt/denovo_a/groups/denovo/TransAssembly'
Elapsed time: 6 h 13 m 1 s
ERROR: CMD ended with status code 2@kokyriakidis Thank you. I see what the problem is now!
You were using Trans-ABySS version 1.5.5 with ABySS version is 2.1.1, but Trans-ABySS 1.5.x does not support ABySS 2.x.x. To resolve the error that you got earlier, you just need to upgrade your Trans-ABySS to the latest version, clean the directory, and re-run.
kokyriakidis
commented
6 years ago @kmnip Thank you! I will try it and I will report!
Hi,
I tried transabyss (k32) on my university cluster on 40gb RNASeq data, following your short tutorial, and it is stuck because it used all 384gb of the node and also swaped! I think it is really strange to require so much memory! Do you have any thoughts?