Hi
I am running a canu (1.7) assembly of a plant genome (1.3gb) based on 11x PacBio reads. It all goes well till unitigging, when bogart fails with a segmentation fault.
I tried restarting and then I start the entire process fresh, but I am getting the same error.
I would greatly appreaciate some help.
I am running canu in a Linux cluster. The canu command used: '/canu/Linux-amd64/bin/canu -assemble -d /PacBio/ useGrid=false correctedErrorRate=0.105 -pacbio-corrected /PacBio/all_corr_pacbio.fasta genomeSize=1.3g -p HEcanuCorrLo'
The contents of unitigging/4-unitigger/unitigger.err:
==> PARAMETERS.
Resources:
Memory 189 GB
Compute Threads 16 (command line)
Lengths:
Minimum read 0 bases
Minimum overlap 500 bases
Overlap Error Rates:
Graph 0.105 (10.500%)
Max 0.105 (10.500%)
Deviations:
Graph 6.000
Bubble 6.000
Repeat 3.000
Edge Confusion:
Absolute 2100
Percent 200.0000
Unitig Construction:
Minimum intersection 500 bases
Maxiumum placements 2 positions
Debugging Enabled:
(none)
==> LOADING AND FILTERING OVERLAPS.
ReadInfo()-- Using 2138563 reads, no minimum read length used.
OverlapCache()-- limited to 193536MB memory (user supplied).
OverlapCache()-- 16MB for read data.
OverlapCache()-- 81MB for best edges.
OverlapCache()-- 212MB for tigs.
OverlapCache()-- 57MB for tigs - read layouts.
OverlapCache()-- 81MB for tigs - error profiles.
OverlapCache()-- 48384MB for tigs - error profile overlaps.
OverlapCache()-- 19355MB for other processes.
OverlapCache()-- ---------
OverlapCache()-- 68229MB for data structures (sum of above).
OverlapCache()-- ---------
OverlapCache()-- 40MB for overlap store structure.
OverlapCache()-- 125266MB for overlap data.
OverlapCache()-- ---------
OverlapCache()-- 193536MB allowed.
OverlapCache()--
OverlapCache()-- Retain at least 22 overlaps/read, based on 11.28x coverage.
OverlapCache()-- Initial guess at 3838 overlaps/read.
OverlapCache()--
OverlapCache()-- Adjusting for sparse overlaps.
OverlapCache()--
OverlapCache()-- reads loading olaps olaps memory
OverlapCache()-- olaps/read all some loaded free
OverlapCache()-- ---------- ------- ------- ----------- ------- --------
OverlapCache()-- 3838 2126932 11631 134145428 85.20% 123219 MB
OverlapCache()-- 698128 2138563 0 157439780 100.00% 122863 MB
OverlapCache()--
OverlapCache()-- Loading overlaps.
OverlapCache()--
OverlapCache()-- read from store saved in cache
OverlapCache()-- ------------ --------- ------------ ---------
OverlapCache()-- 29347933 (018.64%) 28982507 (018.41%)
OverlapCache()-- 58686018 (037.28%) 57964060 (036.82%)
OverlapCache()-- 86967419 (055.24%) 85908451 (054.57%)
OverlapCache()-- 114979131 (073.03%) 113584331 (072.14%)
OverlapCache()-- 143507013 (091.15%) 141800857 (090.07%)
OverlapCache()-- ------------ --------- ------------ ---------
OverlapCache()-- 157439780 (100.00%) 155583954 (098.82%)
OverlapCache()--
OverlapCache()-- Ignored 1191848 duplicate overlaps.
OverlapCache()--
OverlapCache()-- Symmetrizing overlaps.
OverlapCache()-- Finding missing twins.
OverlapCache()-- Found 119302 missing twins in 155583954 overlaps, 1620 are strong.
OverlapCache()-- Dropping weak non-twin overlaps; allocated 0 MB scratch space.
OverlapCache()-- Dropped 3422 overlaps; scratch space released.
OverlapCache()-- Adding 115880 missing twin overlaps.
OverlapCache()-- Finished.
BestOverlapGraph()-- allocating best edges (65MB)
BestOverlapGraph()-- finding initial best edges.
BestOverlapGraph()-- filtering suspicious reads.
BestOverlapGraph()-- marked 1626591 reads as suspicious.
BestOverlapGraph()-- filtering high error edges.
BestOverlapGraph()-- filtering reads with lopsided best edges.
BestOverlapGraph()-- filtering spur reads.
BestOverlapGraph()-- detected 276777 spur reads and 1704959 singleton reads.
Failed with 'Segmentation fault'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::97 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()
(null)::0 in (null)()
../../../../../libstdc++-v3/src/c++98/tree.cc::138 in local_Rb_tree_rotate_left()
../../../../../libstdc++-v3/src/c++98/tree.cc::278 in _ZSt29_Rb_tree_insert_and_rebalancebPSt18_Rb_tree_node_baseS0_RS_()
/usr/include/c++/4.8/bits/stl_tree.h::1025 in _ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE10_M_insert_EPSt18_Rb_tree_node_baseS7_RKj()
/usr/include/c++/4.8/bits/stl_tree.h::1382 in _ZNSt8_Rb_treeIjjSt9_IdentityIjESt4lessIjESaIjEE16_M_insert_uniqueERKj()
/usr/include/c++/4.8/bits/stl_set.h::463 in _ZNSt3setIjSt4lessIjESaIjEE6insertERKj()
bogart/AS_BAT_BestOverlapGraph.C::417 in _ZN16BestOverlapGraph11findZombiesEPKc._omp_fn.3()
../../../libgomp/team.c::116 in gomp_thread_start()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
The contents of the 'log file':
-- Canu snapshot v1.7 +23 changes (r8715 967fcea3c70699eaccc92ff5bfe36d9d10e65a55)
--
-- CITATIONS
--
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
--
-- Read and contig alignments during correction, consensus and GFA building use:
-- Šošic M, Šikic M.
-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
-- Bioinformatics. 2017 May 1;33(9):1394-1395.
-- http://doi.org/10.1093/bioinformatics/btw753
--
-- Overlaps are generated using:
-- Berlin K, et al.
-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
-- Nat Biotechnol. 2015 Jun;33(6):623-30.
-- http://doi.org/10.1038/nbt.3238
--
-- Myers EW, et al.
-- A Whole-Genome Assembly of Drosophila.
-- Science. 2000 Mar 24;287(5461):2196-204.
-- http://doi.org/10.1126/science.287.5461.2196
--
-- Li H.
-- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
-- Bioinformatics. 2016 Jul 15;32(14):2103-10.
-- http://doi.org/10.1093/bioinformatics/btw152
--
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
-- Chin CS, et al.
-- Phased diploid genome assembly with single-molecule real-time sequencing.
-- Nat Methods. 2016 Dec;13(12):1050-1054.
-- http://doi.org/10.1038/nmeth.4035
--
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
-- Chin CS, et al.
-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
-- Nat Methods. 2013 Jun;10(6):563-9
-- http://doi.org/10.1038/nmeth.2474
--
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '1.8.0_92' (from '/net/gmi.oeaw.ac.at/software/mendel/intel-x86_64-sandybridge-avx/software/Java/1.8.0_92/bin/java').
-- Detected gnuplot version '4.6 patchlevel 0' (from 'gnuplot') and image format 'svg'.
-- Detected 16 CPUs and 189 gigabytes of memory.
-- No grid engine detected, grid disabled.
--
-- (tag)Concurrency
-- (tag)Threads |
-- (tag)Memory | |
-- (tag) | | | total usage algorithm
-- ------- ------ -------- -------- ----------------- -----------------------------
-- Local: meryl 189 GB 16 CPUs x 1 job 189 GB 16 CPUs (k-mer counting)
-- Local: cormhap 32 GB 16 CPUs x 1 job 32 GB 16 CPUs (overlap detection with mhap)
-- Local: obtovl 16 GB 16 CPUs x 1 job 16 GB 16 CPUs (overlap detection)
-- Local: utgovl 16 GB 16 CPUs x 1 job 16 GB 16 CPUs (overlap detection)
-- Local: ovb 4 GB 1 CPU x 16 jobs 64 GB 16 CPUs (overlap store bucketizer)
-- Local: ovs 32 GB 1 CPU x 5 jobs 160 GB 5 CPUs (overlap store sorting)
-- Local: red 8 GB 4 CPUs x 4 jobs 32 GB 16 CPUs (read error detection)
-- Local: oea 4 GB 1 CPU x 16 jobs 64 GB 16 CPUs (overlap error adjustment)
-- Local: bat 189 GB 16 CPUs x 1 job 189 GB 16 CPUs (contig construction)
-- Local: gfa 16 GB 16 CPUs x 1 job 16 GB 16 CPUs (GFA alignment and processing)
--
-- In 'HEcanuCorrLo.gkpStore', found PacBio reads:
-- Raw: 0
-- Corrected: 2138563
-- Trimmed: 2138563
--
-- Generating assembly 'HEcanuCorrLo' in '/lustre/scratch/users/ovidiu.paun/PacBio'
--
-- Parameters:
--
-- genomeSize 1300000000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.2400 ( 24.00%)
-- obtOvlErrorRate 0.1050 ( 10.50%)
-- utgOvlErrorRate 0.1050 ( 10.50%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.3000 ( 30.00%)
-- obtErrorRate 0.1050 ( 10.50%)
-- utgErrorRate 0.1050 ( 10.50%)
-- cnsErrorRate 0.1050 ( 10.50%)
--
--
-- BEGIN ASSEMBLY
--
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'utgovl' concurrent execution on Sun Mar 25 23:09:59 2018 with 15192.636 GB free disk space (16 processes; 1 concurrently)
cd unitigging/1-overlapper
./overlap.sh 28 > ./overlap.000028.out 2>&1
./overlap.sh 29 > ./overlap.000029.out 2>&1
./overlap.sh 30 > ./overlap.000030.out 2>&1
./overlap.sh 31 > ./overlap.000031.out 2>&1
./overlap.sh 32 > ./overlap.000032.out 2>&1
./overlap.sh 33 > ./overlap.000033.out 2>&1
./overlap.sh 34 > ./overlap.000034.out 2>&1
./overlap.sh 35 > ./overlap.000035.out 2>&1
./overlap.sh 36 > ./overlap.000036.out 2>&1
./overlap.sh 37 > ./overlap.000037.out 2>&1
./overlap.sh 38 > ./overlap.000038.out 2>&1
./overlap.sh 39 > ./overlap.000039.out 2>&1
./overlap.sh 40 > ./overlap.000040.out 2>&1
./overlap.sh 41 > ./overlap.000041.out 2>&1
./overlap.sh 42 > ./overlap.000042.out 2>&1
./overlap.sh 43 > ./overlap.000043.out 2>&1
-- Finished on Wed Mar 28 18:12:47 2018 (241368 seconds) with 14171.596 GB free disk space
----------------------------------------
-- Found 43 overlapInCore output files.
--
-- overlapInCore compute 'unitigging/1-overlapper':
-- kmer hits
-- with no overlap 45501570067 6048.06977 +- 620223540.657
-- with an overlap 78719890 5.11627907 +- 1063541.313
--
-- overlaps 78719890 5.11627907 +- 1063541.313
-- contained 26906585 .534883721 +- 377754.298
-- dovetail 51813305 0.58139535 +- 686550.596
--
-- overlaps rejected
-- multiple per pair 0 0 +- 0
-- bad short window 0 0 +- 0
-- bad long window 0 0 +- 0
----------------------------------------
-- Starting command on Wed Mar 28 18:12:47 2018 with 14171.596 GB free disk space
cd unitigging
/canu/Linux-amd64/bin/ovStoreBuild \
-O ./HEcanuCorrLo.ovlStore.BUILDING \
-G ./HEcanuCorrLo.gkpStore \
-M 4-32 \
-L ./1-overlapper/ovljob.files \
> ./HEcanuCorrLo.ovlStore.err 2>&1
-- Finished on Wed Mar 28 18:15:10 2018 (143 seconds) with 14152.947 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Wed Mar 28 18:15:10 2018 with 14152.947 GB free disk space
cd unitigging
/canu/Linux-amd64/bin/ovStoreDump \
-G ./HEcanuCorrLo.gkpStore \
-O ./HEcanuCorrLo.ovlStore \
-d -counts \
> ./HEcanuCorrLo.ovlStore/counts.dat 2> ./HEcanuCorrLo.ovlStore/counts.err
-- Finished on Wed Mar 28 18:15:11 2018 (1 second) with 14152.947 GB free disk space
----------------------------------------
--
-- Overlap store 'unitigging/HEcanuCorrLo.ovlStore' successfully constructed.
-- Found 157439780 overlaps for 550391 reads; 1588172 reads have no overlaps.
--
--
-- Purged 1.572 GB in 129 overlap output files.
----------------------------------------
-- Starting command on Wed Mar 28 18:15:14 2018 with 14152.39 GB free disk space
cd unitigging
/canu/Linux-amd64/bin/ovStoreStats \
-G ./HEcanuCorrLo.gkpStore \
-O ./HEcanuCorrLo.ovlStore \
-C 11 \
-o ./HEcanuCorrLo.ovlStore \
> ./HEcanuCorrLo.ovlStore.summary.err 2>&1
-- Finished on Wed Mar 28 18:16:05 2018 (51 seconds) with 14148.996 GB free disk space
----------------------------------------
--
-- Overlap store 'unitigging/HEcanuCorrLo.ovlStore' contains:
--
-- category reads % read length feature size or coverage analysis
-- ---------------- ------- ------- ---------------------- ------------------------ --------------------
-- middle-missing 77125 3.61 11221.40 +- 6346.65 3338.89 +- 3694.25 (bad trimming)
-- middle-hump 61626 2.88 11920.87 +- 6178.76 9550.08 +- 6039.32 (bad trimming)
-- no-5-prime 180664 8.45 7729.42 +- 4847.88 5592.58 +- 4630.36 (bad trimming)
-- no-3-prime 99962 4.67 7417.30 +- 4463.44 5276.57 +- 4241.36 (bad trimming)
--
-- low-coverage 16160 0.76 3561.37 +- 2421.01 1.75 +- 0.76 (easy to assemble, potential for lower quality consensus)
-- unique 16974 0.79 3741.52 +- 2491.78 8.00 +- 2.99 (easy to assemble, perfect, yay)
-- repeat-cont 61443 2.87 5770.34 +- 3660.59 929.18 +- 1259.15 (potential for consensus errors, no impact on assembly)
-- repeat-dove 632 0.03 15601.24 +- 7152.88 453.37 +- 581.10 (hard to assemble, likely won't assemble correctly or even at all)
--
-- span-repeat 5299 0.25 6810.68 +- 3631.66 2594.70 +- 2564.25 (read spans a large repeat, usually easy to assemble)
-- uniq-repeat-cont 20664 0.97 5177.34 +- 3198.95 (should be uniquely placed, low potential for consensus errors, no impact on assembly)
-- uniq-repeat-dove 4807 0.22 8171.09 +- 4468.72 (will end contigs, potential to misassemble)
-- uniq-anchor 5035 0.24 9108.13 +- 4910.64 1420.18 +- 1816.33 (repeat read, with unique section, probable bad read)
--
-- Loading read lengths.
-- Loading number of overlaps per read.
--
-- Configure RED for 8gb memory.
-- Batches of at most (unlimited) reads.
-- 500000000 bases.
-- Expecting evidence of at most 751708149 bases per iteration.
--
-- Total Reads Olaps Evidence
-- Job Memory Read Range Reads Bases Memory Olaps Memory Memory (Memory in MB)
-- ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
-- 1 8192.02 1-53236 53236 406751735 4656.58 4690102 53.67 1433.77
-- 2 8192.03 53237-108640 55404 407058176 4660.15 4378311 50.11 1433.77
-- 3 8192.06 108641-165681 57041 407060655 4660.23 4373937 50.06 1433.77
-- 4 8192.20 165682-223579 57898 406926469 4658.73 4517802 51.70 1433.77
-- 5 8192.02 223580-281937 58358 406768637 4656.93 4658623 53.31 1433.77
-- 6 8192.02 281938-340027 58090 407147650 4661.26 4280241 48.98 1433.77
-- 7 8192.03 340028-398170 58143 406903129 4658.47 4525458 51.79 1433.77
-- 8 8192.02 398171-456141 57971 406961128 4659.12 4467801 51.13 1433.77
-- 9 8192.06 456142-514312 58171 407007916 4659.67 4423468 50.62 1433.77
-- 10 8192.02 514313-572003 57691 407213170 4662.00 4215923 48.25 1433.77
-- 11 8192.03 572004-628990 56987 407220443 4662.06 4211870 48.20 1433.77
-- 12 8192.01 628991-684956 55966 407046114 4660.03 4386794 50.20 1433.77
-- 13 8192.11 684957-743122 58166 406875055 4658.15 4560387 52.19 1433.77
-- 14 8192.07 743123-801973 58851 407168672 4661.53 4261673 48.77 1433.77
-- 15 8192.12 801974-860697 58724 407244086 4662.39 4191514 47.97 1433.77
-- 16 8192.01 860698-919443 58746 406938801 4658.89 4486500 51.34 1433.77
-- 17 8192.08 919444-977503 58060 407058542 4660.24 4374867 50.07 1433.77
-- 18 8192.04 977504-1034412 56909 407141746 4661.16 4291247 49.11 1433.77
-- 19 8192.23 1034413-1090958 56546 407051103 4660.11 4399832 50.35 1433.77
-- 20 8192.02 1090959-1150102 59144 407180421 4661.67 4244928 48.58 1433.77
-- 21 8192.05 1150103-1210676 60574 407327615 4663.40 4096032 46.88 1433.77
-- 22 8192.10 1210677-1271576 60900 407364754 4663.84 4062336 46.49 1433.77
-- 23 8192.29 1271577-1332469 60893 407401180 4664.25 4042686 46.26 1433.77
-- 24 8192.01 1332470-1392863 60394 407183726 4661.75 4237685 48.50 1433.77
-- 25 8192.06 1392864-1453334 60471 407245779 4662.46 4179038 47.83 1433.77
-- 26 8192.08 1453335-1513091 59757 407093086 4660.69 4335507 49.62 1433.77
-- 27 8192.01 1513092-1572596 59505 406820379 4657.56 4603248 52.68 1433.77
-- 28 8192.17 1572597-1631900 59304 406782920 4657.13 4655267 53.28 1433.77
-- 29 8192.00 1631901-1691702 59802 406834482 4657.73 4587501 52.50 1433.77
-- 30 8192.05 1691703-1753446 61744 406920733 4658.78 4499911 51.50 1433.77
-- 31 8192.08 1753447-1817396 63950 406924947 4658.90 4492130 51.41 1433.77
-- 32 8192.09 1817397-1881863 64467 407192994 4661.98 4223568 48.33 1433.77
-- 33 8192.10 1881864-1946497 64634 407068661 4660.57 4348615 49.77 1433.77
-- 34 8192.10 1946498-2011054 64557 407341488 4663.69 4076124 46.65 1433.77
-- 35 8192.11 2011055-2074416 63362 406965302 4659.34 4456528 51.00 1433.77
-- 36 8192.02 2074417-2136642 62226 406949112 4659.12 4467353 51.12 1433.77
-- 37 3633.09 2136643-2138563 1921 13082253 149.77 134973 1.54 1433.77
-- ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
-- 14667223059 157439780
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'red' concurrent execution on Wed Mar 28 18:16:32 2018 with 14147.134 GB free disk space (37 processes; 4 concurrently)
cd unitigging/3-overlapErrorAdjustment
./red.sh 1 > ./red.000001.out 2>&1
./red.sh 2 > ./red.000002.out 2>&1
./red.sh 3 > ./red.000003.out 2>&1
./red.sh 4 > ./red.000004.out 2>&1
./red.sh 5 > ./red.000005.out 2>&1
./red.sh 6 > ./red.000006.out 2>&1
./red.sh 7 > ./red.000007.out 2>&1
./red.sh 8 > ./red.000008.out 2>&1
./red.sh 9 > ./red.000009.out 2>&1
./red.sh 10 > ./red.000010.out 2>&1
./red.sh 11 > ./red.000011.out 2>&1
./red.sh 12 > ./red.000012.out 2>&1
./red.sh 13 > ./red.000013.out 2>&1
./red.sh 14 > ./red.000014.out 2>&1
./red.sh 15 > ./red.000015.out 2>&1
./red.sh 16 > ./red.000016.out 2>&1
./red.sh 17 > ./red.000017.out 2>&1
./red.sh 18 > ./red.000018.out 2>&1
./red.sh 19 > ./red.000019.out 2>&1
./red.sh 20 > ./red.000020.out 2>&1
./red.sh 21 > ./red.000021.out 2>&1
./red.sh 22 > ./red.000022.out 2>&1
./red.sh 23 > ./red.000023.out 2>&1
./red.sh 24 > ./red.000024.out 2>&1
./red.sh 25 > ./red.000025.out 2>&1
./red.sh 26 > ./red.000026.out 2>&1
./red.sh 27 > ./red.000027.out 2>&1
./red.sh 28 > ./red.000028.out 2>&1
./red.sh 29 > ./red.000029.out 2>&1
./red.sh 30 > ./red.000030.out 2>&1
./red.sh 31 > ./red.000031.out 2>&1
./red.sh 32 > ./red.000032.out 2>&1
./red.sh 33 > ./red.000033.out 2>&1
./red.sh 34 > ./red.000034.out 2>&1
./red.sh 35 > ./red.000035.out 2>&1
./red.sh 36 > ./red.000036.out 2>&1
./red.sh 37 > ./red.000037.out 2>&1
-- Finished on Wed Mar 28 19:43:48 2018 (5236 seconds) with 13822.363 GB free disk space
----------------------------------------
-- Found 37 read error detection output files.
--
-- Loading read lengths.
-- Loading number of overlaps per read.
--
-- Configure OEA for 4gb memory.
-- Batches of at most (unlimited) reads.
-- 300000000 bases.
--
-- Total Reads Olaps Adjusts
-- Job Memory Read Range Reads Bases Memory Olaps Memory Memory (Memory in MB)
-- ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
-- 1 3022.12 1-39387 39387 300001809 295.31 3405530 103.93 574.88
-- 2 3019.34 39388-78986 39599 300001730 295.31 3314228 101.14 574.88
-- 3 3013.92 78987-120511 41525 300005698 295.37 3134633 95.66 574.88
-- 4 3021.27 120512-162713 42202 300006623 295.40 3374914 102.99 574.88
-- 5 3015.90 162714-205447 42734 300005738 295.41 3198499 97.61 574.88
-- 6 3025.96 205448-248391 42944 300001634 295.41 3527889 107.66 574.88
-- 7 3018.78 248392-291146 42755 300000693 295.41 3292801 100.49 574.88
-- 8 3015.79 291147-334159 43013 300006775 295.42 3194383 97.48 574.88
-- 9 3017.60 334160-376856 42697 300006630 295.41 3254191 99.31 574.88
-- 10 3022.95 376857-419505 42649 300003122 295.41 3429569 104.66 574.88
-- 11 3017.35 419506-462579 43074 300003180 295.42 3245520 99.05 574.88
-- 12 3018.38 462580-505406 42827 300022708 295.43 3278936 100.07 574.88
-- 13 3013.41 505407-547799 42393 300008097 295.40 3117190 95.13 574.88
-- 14 3008.12 547800-590464 42665 300007331 295.41 2943476 89.83 574.88
-- 15 3018.79 590465-632166 41702 300007048 295.38 3294131 100.53 574.88
-- 16 3017.18 632167-673187 41021 300000621 295.35 3242224 98.94 574.88
-- 17 3017.94 673188-715932 42745 300004316 295.41 3265342 99.65 574.88
-- 18 3023.90 715933-758883 42951 300022712 295.43 3459705 105.58 574.88
-- 19 3010.15 758884-802258 43375 300006622 295.43 3009352 91.84 574.88
-- 20 3013.10 802259-845562 43304 300004264 295.43 3106071 94.79 574.88
-- 21 3018.56 845563-888981 43419 300011068 295.44 3284750 100.24 574.88
-- 22 3015.40 888982-932138 43157 300001161 295.42 3181821 97.10 574.88
-- 23 3017.36 932139-974885 42747 300002388 295.41 3246240 99.07 574.88
-- 24 3014.79 974886-1016930 42045 300003372 295.39 3162788 96.52 574.88
-- 25 3012.00 1016931-1058658 41728 300003312 295.38 3071756 93.74 574.88
-- 26 3019.50 1058659-1100376 41718 300003579 295.38 3317371 101.24 574.88
-- 27 3014.53 1100377-1144201 43825 300005645 295.45 3152457 96.21 574.88
-- 28 3010.42 1144202-1188614 44413 300001584 295.46 3017350 92.08 574.88
-- 29 3012.34 1188615-1233389 44775 300009590 295.48 3079485 93.98 574.88
-- 30 3007.96 1233390-1278361 44972 300011643 295.49 2935869 89.60 574.88
-- 31 3009.54 1278362-1323247 44886 300001380 295.47 2988071 91.19 574.88
-- 32 3013.02 1323248-1367846 44599 300004461 295.47 3102057 94.67 574.88
-- 33 3012.70 1367847-1412070 44224 300014065 295.47 3091839 94.36 574.88
-- 34 3012.25 1412071-1456755 44685 300006820 295.47 3076846 93.90 574.88
-- 35 3017.97 1456756-1500798 44043 300003167 295.45 3265019 99.64 574.88
-- 36 3020.15 1500799-1544662 43864 300009600 295.45 3336422 101.82 574.88
-- 37 3020.66 1544663-1588578 43916 300002472 295.44 3353143 102.33 574.88
-- 38 3023.31 1588579-1632227 43649 300011383 295.45 3440228 104.99 574.88
-- 39 3023.18 1632228-1676299 44072 300006196 295.45 3435557 104.84 574.88
-- 40 3023.69 1676300-1721098 44799 300006682 295.48 3451504 105.33 574.88
-- 41 3015.36 1721099-1767180 46082 300003784 295.51 3177516 96.97 574.88
-- 42 3018.60 1767181-1814386 47206 300007039 295.55 3282206 100.16 574.88
-- 43 3015.36 1814387-1861924 47538 300006251 295.56 3175976 96.92 574.88
-- 44 3017.75 1861925-1909502 47578 300010111 295.56 3254158 99.31 574.88
-- 45 3011.11 1909503-1957203 47701 300007354 295.57 3036325 92.66 574.88
-- 46 3007.58 1957204-2004771 47568 300000013 295.55 2920950 89.14 574.88
-- 47 3019.55 2004772-2051632 46861 300026111 295.56 3313293 101.11 574.88
-- 48 3016.49 2051633-2097750 46118 300007429 295.52 3214236 98.09 574.88
-- 49 2977.79 2097751-2138563 40813 266908048 263.79 2985963 91.12 574.88
-- ---- -------- ------------------- --------- ------------ -------- ------------ -------- --------
-- 14667223059 157439780
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'oea' concurrent execution on Wed Mar 28 19:44:17 2018 with 13821.989 GB free disk space (49 processes; 16 concurrently)
cd unitigging/3-overlapErrorAdjustment
./oea.sh 1 > ./oea.000001.out 2>&1
./oea.sh 2 > ./oea.000002.out 2>&1
./oea.sh 3 > ./oea.000003.out 2>&1
./oea.sh 4 > ./oea.000004.out 2>&1
./oea.sh 5 > ./oea.000005.out 2>&1
./oea.sh 6 > ./oea.000006.out 2>&1
./oea.sh 7 > ./oea.000007.out 2>&1
./oea.sh 8 > ./oea.000008.out 2>&1
./oea.sh 9 > ./oea.000009.out 2>&1
./oea.sh 10 > ./oea.000010.out 2>&1
./oea.sh 11 > ./oea.000011.out 2>&1
./oea.sh 12 > ./oea.000012.out 2>&1
./oea.sh 13 > ./oea.000013.out 2>&1
./oea.sh 14 > ./oea.000014.out 2>&1
./oea.sh 15 > ./oea.000015.out 2>&1
./oea.sh 16 > ./oea.000016.out 2>&1
./oea.sh 17 > ./oea.000017.out 2>&1
./oea.sh 18 > ./oea.000018.out 2>&1
./oea.sh 19 > ./oea.000019.out 2>&1
./oea.sh 20 > ./oea.000020.out 2>&1
./oea.sh 21 > ./oea.000021.out 2>&1
./oea.sh 22 > ./oea.000022.out 2>&1
./oea.sh 23 > ./oea.000023.out 2>&1
./oea.sh 24 > ./oea.000024.out 2>&1
./oea.sh 25 > ./oea.000025.out 2>&1
./oea.sh 26 > ./oea.000026.out 2>&1
./oea.sh 27 > ./oea.000027.out 2>&1
./oea.sh 28 > ./oea.000028.out 2>&1
./oea.sh 29 > ./oea.000029.out 2>&1
./oea.sh 30 > ./oea.000030.out 2>&1
./oea.sh 31 > ./oea.000031.out 2>&1
./oea.sh 32 > ./oea.000032.out 2>&1
./oea.sh 33 > ./oea.000033.out 2>&1
./oea.sh 34 > ./oea.000034.out 2>&1
./oea.sh 35 > ./oea.000035.out 2>&1
./oea.sh 36 > ./oea.000036.out 2>&1
./oea.sh 37 > ./oea.000037.out 2>&1
./oea.sh 38 > ./oea.000038.out 2>&1
./oea.sh 39 > ./oea.000039.out 2>&1
./oea.sh 40 > ./oea.000040.out 2>&1
./oea.sh 41 > ./oea.000041.out 2>&1
./oea.sh 42 > ./oea.000042.out 2>&1
./oea.sh 43 > ./oea.000043.out 2>&1
./oea.sh 44 > ./oea.000044.out 2>&1
./oea.sh 45 > ./oea.000045.out 2>&1
./oea.sh 46 > ./oea.000046.out 2>&1
./oea.sh 47 > ./oea.000047.out 2>&1
./oea.sh 48 > ./oea.000048.out 2>&1
./oea.sh 49 > ./oea.000049.out 2>&1
-- Finished on Wed Mar 28 21:23:32 2018 (5955 seconds) with 14531.423 GB free disk space
----------------------------------------
-- Found 49 overlap error adjustment output files.
----------------------------------------
-- Starting command on Wed Mar 28 21:23:32 2018 with 14531.423 GB free disk space
cd unitigging/3-overlapErrorAdjustment
/canu/Linux-amd64/bin/ovStoreBuild \
-G ../HEcanuCorrLo.gkpStore \
-O ../HEcanuCorrLo.ovlStore \
-evalues \
-L ./oea.files \
> ./oea.apply.err 2>&1
-- Finished on Wed Mar 28 21:23:33 2018 (1 second) with 14531.423 GB free disk space
----------------------------------------
-- No report available.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Wed Mar 28 21:23:33 2018 with 14531.423 GB free disk space (1 processes; 1 concurrently)
cd unitigging/4-unitigger
./unitigger.sh 1 > ./unitigger.000001.out 2>&1
-- Finished on Wed Mar 28 21:24:37 2018 (64 seconds) with 14526.822 GB free disk space
----------------------------------------
--
-- Bogart failed, retry
--
--
-- Running jobs. Second attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Wed Mar 28 21:24:37 2018 with 14526.822 GB free disk space (1 processes; 1 concurrently)
cd unitigging/4-unitigger
./unitigger.sh 1 > ./unitigger.000001.out 2>&1
-- Finished on Wed Mar 28 21:25:36 2018 (59 seconds) with 14537.416 GB free disk space
----------------------------------------
--
-- Bogart failed, tried 2 times, giving up.
--
ABORT:
ABORT: Canu snapshot v1.7 +23 changes (r8715 967fcea3c70699eaccc92ff5bfe36d9d10e65a55)
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting. If that doesn't work, ask for help.
ABORT:
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4