wengan icon indicating copy to clipboard operation
wengan copied to clipboard

Published 20 hours ago • verified publisher icon adigenova

SPolished.asm.wengan.fasta] Error 136

Open josemolina6 opened this issue 3 years ago • 3 comments
trafficstars

Hello, i just installed Wengan and im having this problem. Im running Wengan in a cluster in a single node!

Command: perl /opt/BIO/wengan-0.2/wengan.pl -x ontraw -a A -s R-subs-0.1-1P.fastq.gz,R-subs-0.1-2P.fastq.gz -l PaeAG1-long.fastq.gz -p ensamblaje-wengan -t 20 -g 7000000

Problem: perl /opt/BIO/wengan-0.2/wengan.pl -x ontraw -a M -s R-subs-0.1-1P.fastq.gz,R-subs-0.1-2P.fastq.gz -l PaeAG1-long.fastq.gz -p ensamblaje-wengan -g 7000000 /opt/BIO/wengan-0.2/bin/liger --mlp 10000 -t 1 -c ensamblaje-wengan.MBC7.msplit.fa -l longreads.ensamblaje-wengan1.fa -d ensamblaje-wengan.MBC7.msplit.cov.txt -p ensamblaje-wengan -s ensamblaje-wengan.sams.txt 2>ensamblaje-wengan.liger.err >ensamblaje-wengan.liger.log make: *** [ensamblaje-wengan.mk:79: ensamblaje-wengan.SPolished.asm.wengan.fasta] Error 136

josemolina6 avatar Oct 12 '22 19:10 josemolina6

Hi Jose,

Can you share additional log files or error, from your message I just can infer that the assembly failed at the last step. thanks in advance, Alex

adigenova avatar Oct 12 '22 19:10 adigenova

Hello, thanks. is one of these helpful?

best regards!

Dr. Jose Arturo Molina Mora, Ph.D. Microbiólogo bioinformático Tel. (+506) 2511 8646 e-mail: @.*** ORCID: https://orcid.org/0000-0001-9764-4192

Sección de Biología Celular y Molecular, Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica

-. .-. .-. .-. .-. .-. . |||||\ /||||||\ /||||||\ /| |/ ||||||/ ||||||/ ||||| ~ -~ - -~ - -~ -

El 2022-10-12 13:29, adigenova escribió:

Hi Jose,

Can you share additional log files or error, from your message I just can infer that the assembly failed at the last step. thanks in advance, Alex

-- Reply to this email directly, view it on GitHub [1], or unsubscribe [2]. You are receiving this because you authored the thread.Message ID: @.***>

Links:

[1] https://github.com/adigenova/wengan/issues/73#issuecomment-1276642894 [2] https://github.com/notifications/unsubscribe-auth/AHYSLLYJGZFX642EBLC4VOTWC4GSNANCNFSM6AAAAAARDSSZO4 reference=ensamblaje-wengan.minia.contigs.fa queryfile=ensamblaje-wengan.fms.txt Forward file = R-subs-0.1-1P.fastq.gz Reverse file = R-subs-0.1-2P.fastq.gz

Sorting libs by insert size: ensamblaje-wengan1.fm.sam 0 0 358 126 Scaling std: 0 358 36 Lib: 0 Number of pair-ends : 7602 Number of fragments : 2385 Max allowed coverage 7.82556 AVG 4.82556 STD 1 CTG REP 1 =========== Checking Contigs ========= Minimum Base Coverage : 7 Minimum Contig length : 500 Total fragments 2385 Average fragment length 357 Total Examinated bases 698721 Total Validated bases by at least 7 fragments 588 Percetaje of validated bases 0.0841538 Time spent in interval check 0.00182 secs Total LQI intervals detected 1493 Scanning LQI intervals for missassemblies A total of 633 missassemblies were detected from LQI segments MisAssemblies at start = 0 at end = 2, internal = 0 and whole contig = 631 =========== Done =========

reference=ensamblaje-wengan.MBC7.msplit.fa queryfile=ensamblaje-wengan.fml.txt Query file = PaeAG1-long.fastq.gz Lib : ensamblaje-wengan1.I500.fm.sam Lib : ensamblaje-wengan1.I1000.fm.sam Lib : ensamblaje-wengan1.I2000.fm.sam Lib : ensamblaje-wengan1.I3000.fm.sam Lib : ensamblaje-wengan1.I4000.fm.sam Lib : ensamblaje-wengan1.I5000.fm.sam Lib : ensamblaje-wengan1.I6000.fm.sam Lib : ensamblaje-wengan1.I7000.fm.sam Lib : ensamblaje-wengan1.I8000.fm.sam Lib : ensamblaje-wengan1.I10000.fm.sam Lib : ensamblaje-wengan1.I15000.fm.sam Lib : ensamblaje-wengan1.I20000.fm.sam Lib : ensamblaje-wengan1.I30000.fm.sam Lib : ensamblaje-wengan1.I40000.fm.sam Lib : ensamblaje-wengan1.I50000.fm.sam A total of 15 syntethic libraries will be created by FastMin-SG

Sorting libs by insert size: ensamblaje-wengan1.I1000.fm.sam 0 -2147483648 -214748364 ensamblaje-wengan1.I2000.fm.sam 1 -2147483648 -214748364 ensamblaje-wengan1.I3000.fm.sam 2 -2147483648 -214748364 ensamblaje-wengan1.I4000.fm.sam 3 -2147483648 -214748364 ensamblaje-wengan1.I5000.fm.sam 4 -2147483648 -214748364 ensamblaje-wengan1.I6000.fm.sam 5 -2147483648 -214748364 ensamblaje-wengan1.I7000.fm.sam 6 -2147483648 -214748364 ensamblaje-wengan1.I8000.fm.sam 7 -2147483648 -214748364 ensamblaje-wengan1.I10000.fm.sam 8 -2147483648 -214748364 ensamblaje-wengan1.I15000.fm.sam 9 -2147483648 -214748364 ensamblaje-wengan1.I500.fm.sam 10 456 45 ensamblaje-wengan1.I20000.fm.sam 11 20000 2000 ensamblaje-wengan1.I30000.fm.sam 12 30000 3000 ensamblaje-wengan1.I40000.fm.sam 13 40000 4000 ensamblaje-wengan1.I50000.fm.sam 14 50000 5000 Max allowed coverage 7.77 AVG:5.18 STD:1.09864 Limit: 7.77 #REP(ctg):0 Number of BCC: 53 STARTING TRANSITIVE REDUCTION: A total of 0 edges can be reduced, the total weight is 0 ,whit a total lengh of 0 bases Number of iterations in edge reduction: 0 REDUCED GRAPH 53 ORIGINAL GRAPH 53 ENDING TRANSITIVE REDUCTION Matching Done Total Edges :0 input M 0 Edges in matching: 0 MCW: 0 Total W:0 % -nan there is no cicles in the graph Matching COVER GRAPH 53 ORIGINAL GRAPH 53 Number of CC 53 Number of CC 53 Total Reduced edges >= 10000 (bp) = 0 A total of 0 (-nan%) reduced edges were converted to fragments The Physical Coverage represented in the Paths is: -nan Scaffolds length larger than >= 10000 = 0 Max scaffold length =0

Minia 3, git commit 017d23e setting storage type to hdf5 bcalm_algo params, prefix:ensamblaje-wengan.minia.41.unitigs.fa k:41 a:2 minsize:10 threads:20 mintype:1 DSK used 1 passes and 20 partitions prior to queues allocation 13:07:47 memory [current, maxRSS]: [ 714, 792] MB Starting BCALM2 13:07:47 memory [current, maxRSS]: [ 714, 792] MB

Iterated 127037 kmers, among them 8397 were doubled

In this superbucket (containing 2064 active minimizers), sum of time spent in lambda's: 867.0 msecs longest lambda: 4.6 msecs tot time of best scheduling of lambdas: 867.0 msecs best theoretical speedup: 188.0x Done with partition 0 13:07:47 memory [current, maxRSS]: [ 815, 815] MB

Iterated 143346 kmers, among them 9211 were doubled Loaded 1406 doubled kmers for partition 2

In this superbucket (containing 1766 active minimizers), sum of time spent in lambda's: 950.6 msecs longest lambda: 5.2 msecs tot time of best scheduling of lambdas: 950.6 msecs best theoretical speedup: 183.1x Done with partition 2 13:07:47 memory [current, maxRSS]: [ 815, 815] MB

Iterated 142205 kmers, among them 9248 were doubled Loaded 2697 doubled kmers for partition 4

In this superbucket (containing 2079 active minimizers), sum of time spent in lambda's: 1062.2 msecs longest lambda: 5.3 msecs tot time of best scheduling of lambdas: 1062.2 msecs best theoretical speedup: 200.7x Done with partition 4 13:07:48 memory [current, maxRSS]: [ 815, 815] MB

Iterated 147687 kmers, among them 9804 were doubled Loaded 4196 doubled kmers for partition 6

In this superbucket (containing 2268 active minimizers), sum of time spent in lambda's: 1151.6 msecs longest lambda: 5.5 msecs tot time of best scheduling of lambdas: 1151.6 msecs best theoretical speedup: 209.5x Done with partition 6 13:07:48 memory [current, maxRSS]: [ 815, 815] MB

Iterated 146393 kmers, among them 10206 were doubled Loaded 6285 doubled kmers for partition 8

In this superbucket (containing 3451 active minimizers), sum of time spent in lambda's: 1147.3 msecs longest lambda: 3.6 msecs tot time of best scheduling of lambdas: 1147.3 msecs best theoretical speedup: 320.8x Done with partition 8 13:07:48 memory [current, maxRSS]: [ 815, 815] MB

Iterated 153762 kmers, among them 10925 were doubled Loaded 8957 doubled kmers for partition 10

In this superbucket (containing 3921 active minimizers), sum of time spent in lambda's: 1236.9 msecs longest lambda: 3.0 msecs tot time of best scheduling of lambdas: 1236.9 msecs best theoretical speedup: 413.3x Done with partition 10 13:07:48 memory [current, maxRSS]: [ 815, 815] MB

Iterated 153646 kmers, among them 13153 were doubled Loaded 13028 doubled kmers for partition 12

In this superbucket (containing 6262 active minimizers), sum of time spent in lambda's: 1263.5 msecs longest lambda: 3.8 msecs tot time of best scheduling of lambdas: 1263.5 msecs best theoretical speedup: 329.4x Done with partition 12 13:07:49 memory [current, maxRSS]: [ 815, 815] MB

Iterated 146216 kmers, among them 13933 were doubled Loaded 16547 doubled kmers for partition 14

In this superbucket (containing 8607 active minimizers), sum of time spent in lambda's: 1208.3 msecs longest lambda: 2.9 msecs tot time of best scheduling of lambdas: 1208.3 msecs best theoretical speedup: 423.8x Done with partition 14 13:07:49 memory [current, maxRSS]: [ 815, 815] MB

Iterated 113840 kmers, among them 10243 were doubled Loaded 13642 doubled kmers for partition 16

In this superbucket (containing 6047 active minimizers), sum of time spent in lambda's: 904.9 msecs longest lambda: 2.0 msecs tot time of best scheduling of lambdas: 904.9 msecs best theoretical speedup: 451.6x Done with partition 16 13:07:49 memory [current, maxRSS]: [ 815, 815] MB

Iterated 109292 kmers, among them 12041 were doubled Loaded 17920 doubled kmers for partition 18

In this superbucket (containing 9741 active minimizers), sum of time spent in lambda's: 899.8 msecs longest lambda: 2.3 msecs tot time of best scheduling of lambdas: 899.8 msecs best theoretical speedup: 385.7x Done with partition 18 13:07:49 memory [current, maxRSS]: [ 815, 815] MB Number of sequences in glue: 239068 Number of pre-tips removed : 0 Buckets compaction and gluing : 2.7 secs Within that, creating buckets from superbuckets: 1.5 secs bucket compaction (wall-clock during threads): 1.1 secs

            within all bucket compaction threads,
                   adding nodes to subgraphs: 9.2 secs
     subgraphs constructions and compactions: 9.6 secs
              compacted nodes redistribution: 2.3 secs

Sum of CPU times for bucket compactions: 22.6 secs BCALM total wallclock (excl kmer counting): 2.8 secs Maximum number of kmers in a subgraph: 787 Performance of compaction step:

             Wallclock time spent in parallel section : 1.1 secs
         Best theoretical speedup in parallel section : 302.0x

Best theor. speedup in parallel section using 1 threads : 1.0x Sum of longest bucket compaction for each sb : 0.1 secs Sum of best scheduling for each sb : 21.1 secs Done with all compactions 13:07:50 memory [current, maxRSS]: [ 815, 815] MB bglue_algo params, prefix:ensamblaje-wengan.minia.41.unitigs.fa k:41 threads:20 Starting bglue with 20 threads 13:07:50 memory [current, maxRSS]: [ 815, 815] MB number of sequences to be glued: 239068 13:07:50 memory [current, maxRSS]: [ 815, 815] MB 143888 marked kmers, 47034 unmarked kmers 13:07:50 memory [current, maxRSS]: [ 815, 815] MB created vector of hashes, size approx 1 MB) 13:07:50 memory [current, maxRSS]: [ 815, 815] MB pass 1/3, 71944 unique hashes written to disk, size 0 MB 13:07:50 memory [current, maxRSS]: [ 815, 815] MB 143602 marked kmers, 47034 unmarked kmers 13:07:50 memory [current, maxRSS]: [ 815, 815] MB created vector of hashes, size approx 1 MB) 13:07:50 memory [current, maxRSS]: [ 815, 815] MB pass 2/3, 71801 unique hashes written to disk, size 0 MB 13:07:50 memory [current, maxRSS]: [ 815, 815] MB 143612 marked kmers, 47034 unmarked kmers 13:07:50 memory [current, maxRSS]: [ 815, 815] MB created vector of hashes, size approx 1 MB) 13:07:50 memory [current, maxRSS]: [ 815, 815] MB pass 3/3, 71806 unique hashes written to disk, size 0 MB 13:07:50 memory [current, maxRSS]: [ 815, 815] MB loaded all unique UF elements (215551) into a single vector of size 1 MB 13:07:50 memory [current, maxRSS]: [ 815, 815] MB Bitarray 1021248 bits (100.00 %) (array + ranks ) final hash 0 bits (0.00 %) (nb in final hash 0) UF MPHF constructed (0 MB) 13:07:50 memory [current, maxRSS]: [ 815, 815] MB UF constructed 13:07:50 memory [current, maxRSS]: [ 815, 815] MB freed original UF (1 MB) 13:07:50 memory [current, maxRSS]: [ 815, 815] MB loaded 32-bit UF (0 MB) 13:07:50 memory [current, maxRSS]: [ 815, 815] MB Allowed 95 MB memory for buffers 13:07:50 memory [current, maxRSS]: [ 815, 815] MB Disk partitioning of glue 13:07:50 memory [current, maxRSS]: [ 815, 815] MB Done disk partitioning of glue 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Top 10 glue partitions by size: Glue partition 1218 has 422 sequences Glue partition 1515 has 363 sequences Glue partition 1994 has 288 sequences Glue partition 461 has 270 sequences Glue partition 92 has 261 sequences Glue partition 1096 has 260 sequences Glue partition 514 has 260 sequences Glue partition 747 has 259 sequences Glue partition 931 has 258 sequences Glue partition 1010 has 257 sequences Glueing partitions 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 0 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 20 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 40 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 60 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 80 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 100 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 120 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 140 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 160 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 180 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 200 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 220 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 240 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 260 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 280 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 300 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 320 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 340 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 360 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 380 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 400 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 420 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 440 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 460 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 480 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 500 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 520 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 540 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 560 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 580 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 600 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 620 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 640 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 660 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 680 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 700 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 720 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 740 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 760 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 780 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 800 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 820 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 840 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 860 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 880 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 900 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 920 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 940 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 960 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 980 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1000 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1020 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1040 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1060 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1080 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1100 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1120 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1140 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1160 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1180 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1200 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1220 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1240 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1260 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1280 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1300 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1320 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1340 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1360 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1380 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1400 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1420 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1440 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1460 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1480 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1500 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1520 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1540 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1560 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1580 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1600 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1620 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1640 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1660 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1680 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1700 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1720 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1740 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1760 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1780 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1800 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1820 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1840 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1860 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1880 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1900 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1920 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1940 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1960 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Gluing partition 1980 (size: 0 MB) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB end 13:07:51 memory [current, maxRSS]: [ 815, 815] MB debug: not deleting glue files Finding links between unitigs 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 0 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (2438kmers/2468extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 1 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (8029kmers/8112extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 2 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (348kmers/352extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 3 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (2806kmers/2852extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 4 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (6694kmers/6824extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 5 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (17298kmers/17546extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 6 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (1065kmers/1079extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 7 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (7689kmers/7801extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB gathering links from disk 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Done finding links between unitigs 13:07:51 memory [current, maxRSS]: [ 815, 815] MB iterating on 46757 nodes on disk NodesDeleter mem usage prior to flush: 0 MB 294 tips removed. 45525 tip candidates passed degree check. Tips timings: 0.2 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.1 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 21 tips removed. 45304 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 9 tips removed. 45301 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 3 tips removed. 45299 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 24 bulges removed. 145/32+113 any=long+short simple path examined across all threads, among them 96 topological bulges, 0+0 were first-node duplicates. 87 bulges candidates passed degree check. 1+0+1 without alt. path (complex+loop+noend), 46 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 22). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 bulges removed. 78/34+44 any=long+short simple path examined across all threads, among them 28 topological bulges, 0+0 were first-node duplicates. 39 bulges candidates passed degree check. 0+0+0 without alt. path (complex+loop+noend), 28 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 0). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 bulges removed. 78/34+44 any=long+short simple path examined across all threads, among them 28 topological bulges, 0+0 were first-node duplicates. 39 bulges candidates passed degree check. 0+0+0 without alt. path (complex+loop+noend), 28 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 0). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 39 EC candidates passed degree check. 78/6+72 any=long+short simple path examined across all threads 36 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 39 EC candidates passed degree check. 78/6+72 any=long+short simple path examined across all threads 36 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 39 EC candidates passed degree check. 78/6+72 any=long+short simple path examined across all threads 36 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 2 tips removed. 45299 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 bulges removed. 76/34+42 any=long+short simple path examined across all threads, among them 28 topological bulges, 0+0 were first-node duplicates. 38 bulges candidates passed degree check. 0+0+0 without alt. path (complex+loop+noend), 28 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 0). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 46757 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 38 EC candidates passed degree check. 76/6+70 any=long+short simple path examined across all threads 36 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. Finding links between unitigs 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 0 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (984kmers/990extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 1 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (3226kmers/3230extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 2 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (151kmers/151extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 3 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (1168kmers/1174extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 4 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (2769kmers/2793extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 5 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (6786kmers/6812extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 6 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (453kmers/453extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 1 pass 7 13:07:51 memory [current, maxRSS]: [ 815, 815] MB step 2 (3146kmers/3163extremities) 13:07:51 memory [current, maxRSS]: [ 815, 815] MB gathering links from disk 13:07:51 memory [current, maxRSS]: [ 815, 815] MB Done finding links between unitigs 13:07:51 memory [current, maxRSS]: [ 815, 815] MB -in : ensamblaje-wengan.minia_reads.41.txt -kmer-size : 41 -abundance-min : 2 -out : ensamblaje-wengan.minia.41 -minimizer-size : 10 -max-memory : 5000 -nb-cores : 20 -traversal : contig -fasta-line : 0 -tip-len-topo-kmult : 2.500000 -tip-len-rctc-kmult : 10.000000 -tip-rctc-cutoff : 2.000000 -bulge-len-kmult : 3.000000 -bulge-len-kadd : 100 -bulge-altpath-kadd : 50 -bulge-altpath-covmult : 1 -ec-len-kmult : 9.000000 -ec-rctc-cutoff : 4.000000 -abundance-max : 2147483647 -abundance-min-threshold : 2 -histo-max : 10000 -solidity-kind : sum -max-disk : 0 -out-dir : . -out-tmp : . -out-compress : 0 -storage-type : hdf5 -histo2D : 0 -histo : 0 -minimizer-type : 1 -repartition-type : 1 -bloom : neighbor -debloom : cascading -debloom-impl : minimizer -branching-nodes : stored -topology-stats : 0 -verbose : 1 -integer-precision : 0 -nb-glue-partitions : 0 -storage-type : 1 -verbose : 1 -verbose : 1 -verbose : 1 stats
traversal : contig nb_contigs : 9383 nb_small_contigs_discarded : 13582 nt_assembled : 2494433 max_length : 3165 graph simpification stats
tips removed : 294 + 21 + 9 + 3 + 2 bulges removed : 24 + 0 + 0 + 0 EC removed : 0 + 0 + 0 + 0 assembly traversal stats
time : 8.000 assembly : 0.202 graph construction : 7.798

Minia 3, git commit 017d23e setting storage type to hdf5 bcalm_algo params, prefix:ensamblaje-wengan.minia.81.unitigs.fa k:81 a:2 minsize:10 threads:20 mintype:1 DSK used 1 passes and 20 partitions prior to queues allocation 13:07:59 memory [current, maxRSS]: [ 743, 868] MB Starting BCALM2 13:07:59 memory [current, maxRSS]: [ 743, 868] MB

Iterated 96333 kmers, among them 2932 were doubled

In this superbucket (containing 1104 active minimizers), sum of time spent in lambda's: 1313.7 msecs longest lambda: 7.9 msecs tot time of best scheduling of lambdas: 1313.7 msecs best theoretical speedup: 166.9x Done with partition 0 13:08:00 memory [current, maxRSS]: [ 816, 868] MB

Iterated 98326 kmers, among them 2892 were doubled Loaded 666 doubled kmers for partition 2

In this superbucket (containing 1108 active minimizers), sum of time spent in lambda's: 1211.8 msecs longest lambda: 6.9 msecs tot time of best scheduling of lambdas: 1211.8 msecs best theoretical speedup: 175.0x Done with partition 2 13:08:00 memory [current, maxRSS]: [ 816, 868] MB

Iterated 99205 kmers, among them 2894 were doubled Loaded 828 doubled kmers for partition 4

In this superbucket (containing 1002 active minimizers), sum of time spent in lambda's: 1325.5 msecs longest lambda: 9.8 msecs tot time of best scheduling of lambdas: 1325.5 msecs best theoretical speedup: 135.7x Done with partition 4 13:08:00 memory [current, maxRSS]: [ 816, 868] MB

Iterated 97097 kmers, among them 3017 were doubled Loaded 1431 doubled kmers for partition 6

In this superbucket (containing 1446 active minimizers), sum of time spent in lambda's: 1166.5 msecs longest lambda: 6.4 msecs tot time of best scheduling of lambdas: 1166.5 msecs best theoretical speedup: 182.9x Done with partition 6 13:08:00 memory [current, maxRSS]: [ 816, 868] MB

Iterated 97296 kmers, among them 2983 were doubled Loaded 1802 doubled kmers for partition 8

In this superbucket (containing 1481 active minimizers), sum of time spent in lambda's: 1324.8 msecs longest lambda: 10.2 msecs tot time of best scheduling of lambdas: 1324.8 msecs best theoretical speedup: 130.1x Done with partition 8 13:08:01 memory [current, maxRSS]: [ 816, 868] MB

Iterated 98958 kmers, among them 3082 were doubled Loaded 2307 doubled kmers for partition 10

In this superbucket (containing 1579 active minimizers), sum of time spent in lambda's: 1333.5 msecs longest lambda: 7.4 msecs tot time of best scheduling of lambdas: 1333.5 msecs best theoretical speedup: 179.3x Done with partition 10 13:08:01 memory [current, maxRSS]: [ 816, 868] MB

Iterated 98157 kmers, among them 3250 were doubled Loaded 3132 doubled kmers for partition 12

In this superbucket (containing 2310 active minimizers), sum of time spent in lambda's: 1253.8 msecs longest lambda: 5.1 msecs tot time of best scheduling of lambdas: 1253.8 msecs best theoretical speedup: 243.6x Done with partition 12 13:08:01 memory [current, maxRSS]: [ 816, 868] MB

Iterated 99054 kmers, among them 3362 were doubled Loaded 3914 doubled kmers for partition 14

In this superbucket (containing 2680 active minimizers), sum of time spent in lambda's: 1264.6 msecs longest lambda: 4.3 msecs tot time of best scheduling of lambdas: 1264.6 msecs best theoretical speedup: 296.7x Done with partition 14 13:08:01 memory [current, maxRSS]: [ 816, 868] MB

Iterated 99219 kmers, among them 4084 were doubled Loaded 5412 doubled kmers for partition 16

In this superbucket (containing 4224 active minimizers), sum of time spent in lambda's: 1319.7 msecs longest lambda: 3.1 msecs tot time of best scheduling of lambdas: 1319.7 msecs best theoretical speedup: 424.5x Done with partition 16 13:08:02 memory [current, maxRSS]: [ 816, 868] MB

Iterated 94895 kmers, among them 3763 were doubled Loaded 5332 doubled kmers for partition 18

In this superbucket (containing 4590 active minimizers), sum of time spent in lambda's: 1260.1 msecs longest lambda: 2.8 msecs tot time of best scheduling of lambdas: 1260.1 msecs best theoretical speedup: 450.6x Done with partition 18 13:08:02 memory [current, maxRSS]: [ 816, 868] MB Number of sequences in glue: 82582 Number of pre-tips removed : 0 Buckets compaction and gluing : 2.6 secs Within that, creating buckets from superbuckets: 1.2 secs bucket compaction (wall-clock during threads): 1.3 secs

            within all bucket compaction threads,
                   adding nodes to subgraphs: 11.6 secs
     subgraphs constructions and compactions: 12.7 secs
              compacted nodes redistribution: 1.5 secs

Sum of CPU times for bucket compactions: 27.0 secs BCALM total wallclock (excl kmer counting): 2.7 secs Maximum number of kmers in a subgraph: 832 Performance of compaction step:

             Wallclock time spent in parallel section : 1.3 secs
         Best theoretical speedup in parallel section : 253.8x

Best theor. speedup in parallel section using 1 threads : 1.0x Sum of longest bucket compaction for each sb : 0.1 secs Sum of best scheduling for each sb : 25.8 secs Done with all compactions 13:08:02 memory [current, maxRSS]: [ 816, 868] MB bglue_algo params, prefix:ensamblaje-wengan.minia.81.unitigs.fa k:81 threads:20 Starting bglue with 20 threads 13:08:02 memory [current, maxRSS]: [ 816, 868] MB number of sequences to be glued: 82582 13:08:02 memory [current, maxRSS]: [ 816, 868] MB 43916 marked kmers, 32902 unmarked kmers 13:08:02 memory [current, maxRSS]: [ 816, 868] MB created vector of hashes, size approx 0 MB) 13:08:02 memory [current, maxRSS]: [ 816, 868] MB pass 1/3, 21958 unique hashes written to disk, size 0 MB 13:08:02 memory [current, maxRSS]: [ 816, 868] MB 44036 marked kmers, 32902 unmarked kmers 13:08:02 memory [current, maxRSS]: [ 816, 868] MB created vector of hashes, size approx 0 MB) 13:08:02 memory [current, maxRSS]: [ 816, 868] MB pass 2/3, 22018 unique hashes written to disk, size 0 MB 13:08:02 memory [current, maxRSS]: [ 816, 868] MB 44310 marked kmers, 32902 unmarked kmers 13:08:02 memory [current, maxRSS]: [ 816, 868] MB created vector of hashes, size approx 0 MB) 13:08:02 memory [current, maxRSS]: [ 816, 868] MB pass 3/3, 22155 unique hashes written to disk, size 0 MB 13:08:02 memory [current, maxRSS]: [ 816, 868] MB loaded all unique UF elements (66131) into a single vector of size 0 MB 13:08:02 memory [current, maxRSS]: [ 816, 868] MB Bitarray 317312 bits (100.00 %) (array + ranks ) final hash 0 bits (0.00 %) (nb in final hash 0) UF MPHF constructed (0 MB) 13:08:02 memory [current, maxRSS]: [ 817, 868] MB UF constructed 13:08:02 memory [current, maxRSS]: [ 817, 868] MB freed original UF (0 MB) 13:08:02 memory [current, maxRSS]: [ 817, 868] MB loaded 32-bit UF (0 MB) 13:08:02 memory [current, maxRSS]: [ 817, 868] MB Allowed 95 MB memory for buffers 13:08:02 memory [current, maxRSS]: [ 817, 868] MB Disk partitioning of glue 13:08:02 memory [current, maxRSS]: [ 817, 868] MB Done disk partitioning of glue 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Top 10 glue partitions by size: Glue partition 356 has 149 sequences Glue partition 272 has 145 sequences Glue partition 6 has 109 sequences Glue partition 915 has 106 sequences Glue partition 1320 has 103 sequences Glue partition 58 has 102 sequences Glue partition 77 has 98 sequences Glue partition 461 has 97 sequences Glue partition 866 has 96 sequences Glue partition 1621 has 95 sequences Glueing partitions 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 0 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 20 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 40 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 60 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 80 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 100 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 120 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 140 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 160 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 180 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 200 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 220 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 240 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 260 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 280 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 300 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 320 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 340 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 360 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 380 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 400 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 420 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 440 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 460 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 480 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 500 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 520 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 540 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 560 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 580 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 600 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 620 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 640 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 660 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 680 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 700 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 720 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 740 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 760 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 780 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 800 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 820 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 840 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 860 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 880 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 900 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 920 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 940 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 960 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 980 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1000 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1020 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1040 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1060 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1080 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1100 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1120 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1140 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1160 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1180 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1200 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1220 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1240 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1260 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1280 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1300 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1320 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1340 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1360 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1380 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1400 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1420 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1440 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1460 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1480 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1500 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1520 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1540 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1560 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1580 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1600 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1620 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1640 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1660 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1680 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1700 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1720 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1740 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1760 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1780 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1800 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1820 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1840 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1860 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1880 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1900 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1920 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1940 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1960 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Gluing partition 1980 (size: 0 MB) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB end 13:08:03 memory [current, maxRSS]: [ 817, 868] MB debug: not deleting glue files Finding links between unitigs 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 0 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (1686kmers/1706extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 1 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (5919kmers/5979extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 2 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (278kmers/284extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 3 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (2390kmers/2412extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 4 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (4560kmers/4603extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 5 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (11976kmers/12057extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 6 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (522kmers/526extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 1 pass 7 13:08:03 memory [current, maxRSS]: [ 817, 868] MB step 2 (5293kmers/5337extremities) 13:08:03 memory [current, maxRSS]: [ 817, 868] MB gathering links from disk 13:08:03 memory [current, maxRSS]: [ 817, 868] MB Done finding links between unitigs 13:08:03 memory [current, maxRSS]: [ 817, 868] MB iterating on 32721 nodes on disk NodesDeleter mem usage prior to flush: 0 MB 214 tips removed. 32126 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 11 tips removed. 31975 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 tips removed. 31967 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision 0.0 CPUsecs tip processing Nodes deletion: 0.0 CPUsecs. Nodes caching : 0.0 CPUsecs. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 1 bulges removed. 6/1+5 any=long+short simple path examined across all threads, among them 4 topological bulges, 0+0 were first-node duplicates. 3 bulges candidates passed degree check. 0+0+0 without alt. path (complex+loop+noend), 2 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 0). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 bulges removed. 2/1+1 any=long+short simple path examined across all threads, among them 0 topological bulges, 0+0 were first-node duplicates. 1 bulges candidates passed degree check. 0+0+0 without alt. path (complex+loop+noend), 0 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 0). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 bulges removed. 2/1+1 any=long+short simple path examined across all threads, among them 0 topological bulges, 0+0 were first-node duplicates. 1 bulges candidates passed degree check. 0+0+0 without alt. path (complex+loop+noend), 0 didn't satisfy cov. criterion. Bulges timings: 0.0 CPUsecs total. 0.0 CPUsecs simple path traversal. 0.0(/0.0) CPUsecs path-finding(/failed). Longest: 0.0 CPUmillisecs (depth 0). 0.0 CPUsecs topological bulge processing, 0.0 CPUsecs nodes deletion. 0.0 CPUsecs various overhead. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 1 EC candidates passed degree check. 2/0+2 any=long+short simple path examined across all threads 0 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 1 EC candidates passed degree check. 2/0+2 any=long+short simple path examined across all threads 0 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 erroneous connections removed. 1 EC candidates passed degree check. 2/0+2 any=long+short simple path examined across all threads 0 topological ECs. EC Timings: 0.0 CPUsecs total, including 0.0 CPUsecs EC simple paths 0.0 CPUsecs EC coverage test 0.0 CPUsecs EC processing Nodes deletion: 0.0 CPUsecs. iterating on 32721 cached nodes NodesDeleter mem usage prior to flush: 0 MB 0 tips removed. 31967 tip candidates passed degree check. Tips timings: 0.1 CPUsecs total. 0.0 CPUsecs simple path traversal, including: 0.0 CPUsecs long simple paths 0.0 CPUsecs short (topological) simple paths 0.0 CPUsecs short (RCTC) simple paths 0.0 CPUsecs tip decision

josemolina6 avatar Oct 12 '22 19:10 josemolina6

Wengan crash because there are really few contigs and therefore links, it seem that there is an issue with the short-read data. I suggest to assess the quality of the short-read data with:

https://github.com/digenoma-lab/k-count-nf

That will give you an estimate of the genome size and will be helpful to determine the quality of the short-read data. that then you can post here to discuss.

Best, Alex

adigenova avatar Nov 03 '22 21:11 adigenova