Hi,
I'm having a similar issue like #546: #546
The assembly step stops with the following error:
--
-- 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_45' (from '/tools/java/jre1.8.0_45/bin/java').
-- Detected gnuplot version '4.2 patchlevel 6 ' (from 'gnuplot') and image format 'png'.
-- Detected 40 CPUs and 252 gigabytes of memory.
-- Limited to 100G gigabytes from maxMemory option.
-- Limited to 8 CPUs from maxThreads option.
-- Detected Sun Grid Engine in '/SGE/ogs/default'.
-- User supplied Grid Engine environment '-pe parallel_smp THREADS'.
-- Detected Grid Engine consumable 'memoire'.
--
-- Found 1 host with 64 cores and 1009 GB memory under Sun Grid Engine control.
-- Found 1 host with 240 cores and 2932 GB memory under Sun Grid Engine control.
-- Found 1 host with 20 cores and 252 GB memory under Sun Grid Engine control.
-- Found 67 hosts with 40 cores and 252 GB memory under Sun Grid Engine control.
--
-- (tag)Threads
-- (tag)Memory |
-- (tag) | | algorithm
-- ------- ------ -------- -----------------------------
-- Grid: meryl 25 GB 4 CPUs (k-mer counting)
-- Grid: cormhap 13 GB 4 CPUs (overlap detection with mhap)
-- Grid: obtovl 8 GB 4 CPUs (overlap detection)
-- Grid: utgovl 8 GB 4 CPUs (overlap detection)
-- Grid: cor 20 GB 4 CPUs (read correction)
-- Grid: ovb 4 GB 1 CPU (overlap store bucketizer)
-- Grid: ovs 8 GB 1 CPU (overlap store sorting)
-- Grid: red 6 GB 4 CPUs (read error detection)
-- Grid: oea 2 GB 1 CPU (overlap error adjustment)
-- Grid: bat 25 GB 4 CPUs (contig construction)
-- Grid: cns 25 GB 4 CPUs (consensus)
-- Grid: gfa 8 GB 4 CPUs (GFA alignment and processing)
--
-- Found PacBio corrected reads in 'unitigging/Assembly_1.gkpStore'.
--
-- Generating assembly 'Assembly_1' in '/work/project/mildew/Assembly1'
--
-- Parameters:
--
-- genomeSize 100000000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.2400 ( 24.00%)
-- obtOvlErrorRate 0.0450 ( 4.50%)
-- utgOvlErrorRate 0.0450 ( 4.50%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.3000 ( 30.00%)
-- obtErrorRate 0.0450 ( 4.50%)
-- utgErrorRate 0.0450 ( 4.50%)
-- cnsErrorRate 0.0750 ( 7.50%)
--
--
-- BEGIN ASSEMBLY
--
--
-- Bogart failed, tried 2 times, giving up.
--
ABORT:
ABORT: Canu 1.6
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:
Your job has been killed.
This may happen if one of the followings hold :
- you exceeded one of the queue/job limits (run time, memory, etc)
- you (or admin) killed the job using qdel
- something bad happened.
Now, just in case something bad happened, here are the debug information about your job :
total 0
JOB INFO :
total 44
-rw-r--r-- 1 sgeadmin sgeadmin 34 Dec 1 14:29 pe_hostfile
-rw-r--r-- 1 sgeadmin sgeadmin 11911 Dec 1 14:29 environment
-rw-r--r-- 1 sgeadmin sgeadmin 2313 Dec 1 14:29 config
-rw-r--r-- 1 sgeadmin sgeadmin 6 Dec 1 14:29 pid
-rw-r--r-- 1 sgeadmin sgeadmin 6 Dec 1 14:29 job_pid
-rw-r--r-- 1 sgeadmin sgeadmin 6 Dec 1 14:29 addgrpid
-rw-r--r-- 1 agross UMR1202 0 Dec 1 14:29 exit_status
-rw-r--r-- 1 agross UMR1202 0 Dec 1 14:29 error
-rw-r--r-- 1 sgeadmin sgeadmin 318 Dec 1 14:29 usage
-rw-r--r-- 1 agross UMR1202 4781 Dec 1 14:29 trace
STATUS :
TRACE :
12/01/2017 14:29:19 [500:69993]: shepherd called with uid = 0, euid = 500
12/01/2017 14:29:19 [500:69993]: starting up 2011.11p1
12/01/2017 14:29:19 [500:69993]: setpgid(69993, 69993) returned 0
12/01/2017 14:29:19 [500:69993]: do_core_binding: "binding" parameter not found in config file
12/01/2017 14:29:19 [500:69993]: no prolog script to start
12/01/2017 14:29:19 [500:69993]: no pe_start script to start
12/01/2017 14:29:19 [500:69993]: parent: forked "job" with pid 69994
12/01/2017 14:29:19 [500:69993]: parent: job-pid: 69994
12/01/2017 14:29:19 [500:69994]: child: starting son(job, /var/spool/sge/node006/job_scripts/4746155, 0);
12/01/2017 14:29:19 [500:69994]: pid=69994 pgrp=69994 sid=69994 old pgrp=69993 getlogin()=<no login set>
12/01/2017 14:29:19 [500:69994]: reading passwd information for user 'agross'
12/01/2017 14:29:19 [500:69994]: setosjobid: uid = 0, euid = 500
12/01/2017 14:29:19 [500:69994]: setting limits
12/01/2017 14:29:19 [500:69994]: RLIMIT_CPU setting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) resulting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY))
12/01/2017 14:29:19 [500:69994]: RLIMIT_FSIZE setting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) resulting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY))
12/01/2017 14:29:19 [500:69994]: RLIMIT_DATA setting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) resulting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY))
12/01/2017 14:29:19 [500:69994]: RLIMIT_STACK setting: (soft 268435456, hard 268435456) resulting: (soft 268435456, hard 268435456)
12/01/2017 14:29:19 [500:69994]: RLIMIT_CORE setting: (soft 0, hard 0) resulting: (soft 0, hard 0)
12/01/2017 14:29:19 [500:69994]: RLIMIT_MEMLOCK setting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) resulting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY))
12/01/2017 14:29:19 [500:69994]: RLIMIT_VMEM/RLIMIT_AS setting: (soft 8589934592, hard 8589934592) resulting: (soft 8589934592, hard 8589934592)
12/01/2017 14:29:19 [500:69994]: RLIMIT_RSS setting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) resulting: (soft 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY))
12/01/2017 14:29:19 [500:69994]: setting environment
12/01/2017 14:29:19 [500:69994]: Initializing error file
12/01/2017 14:29:19 [500:69994]: switching to intermediate/target user
12/01/2017 14:29:19 [14660:69994]: closing all filedescriptors
12/01/2017 14:29:19 [14660:69994]: further messages are in "error" and "trace"
12/01/2017 14:29:19 [14660:69994]: using stdout as stderr
12/01/2017 14:29:19 [14660:69994]: now running with uid=14660, euid=14660
12/01/2017 14:29:19 [14660:69994]: execvp(/var/spool/sge/node006/job_scripts/4746155, "/var/spool/sge/node006/job_scripts/4746155")
12/01/2017 14:29:22 [500:69993]: wait3 returned 69994 (status: 256; WIFSIGNALED: 0, WIFEXITED: 1, WEXITSTATUS: 1)
12/01/2017 14:29:22 [500:69993]: job exited with exit status 1
12/01/2017 14:29:22 [500:69993]: reaped "job" with pid 69994
12/01/2017 14:29:22 [500:69993]: job exited not due to signal
12/01/2017 14:29:22 [500:69993]: job exited with status 1
12/01/2017 14:29:22 [500:69993]: now sending signal KILL to pid -69994
12/01/2017 14:29:22 [500:69993]: writing usage file to "usage"
12/01/2017 14:29:22 [500:69993]: no tasker to notify
12/01/2017 14:29:22 [500:69993]: no pe_stop script to start
12/01/2017 14:29:22 [500:69993]: parent: forked "epilog" with pid 70127
12/01/2017 14:29:22 [500:69993]: using signal delivery delay of 120 seconds
12/01/2017 14:29:22 [500:69993]: parent: epilog-pid: 70127
12/01/2017 14:29:22 [500:70127]: child: starting son(epilog, /SGE/ogs/inra/tools/epilog_verbose.sh, 0);
12/01/2017 14:29:22 [500:70127]: pid=70127 pgrp=70127 sid=70127 old pgrp=69993 getlogin()=<no login set>
12/01/2017 14:29:22 [500:70127]: reading passwd information for user 'agross'
12/01/2017 14:29:22 [500:70127]: setting limits
12/01/2017 14:29:22 [500:70127]: setting environment
12/01/2017 14:29:22 [500:70127]: Initializing error file
12/01/2017 14:29:22 [500:70127]: switching to intermediate/target user
12/01/2017 14:29:22 [14660:70127]: closing all filedescriptors
12/01/2017 14:29:22 [14660:70127]: further messages are in "error" and "trace"
12/01/2017 14:29:22 [14660:70127]: using "/bin/bash" as shell of user "agross"
12/01/2017 14:29:22 [14660:70127]: using stdout as stderr
12/01/2017 14:29:22 [14660:70127]: now running with uid=14660, euid=14660
12/01/2017 14:29:22 [14660:70127]: execvp(/SGE/ogs/inra/tools/epilog_verbose.sh, "/SGE/ogs/inra/tools/epilog_verbose.sh")
ERROR :
Messages file :
End debugging information.
Epilog : job finished at Fri Dec 1 14:29:29 CET 2017
Because I read that the unitigger.err file could be important to solve the problem, I also attach it here:
Resources:
Memory 25 GB
Compute Threads 4 (command line)
Lengths:
Minimum read 0 bases
Minimum overlap 500 bases
Overlap Error Rates:
Graph 0.045 (4.500%)
Max 0.045 (4.500%)
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 954643 reads, no minimum read length used.
OverlapCache()-- limited to 25600MB memory (user supplied).
OverlapCache()-- 7MB for read data.
OverlapCache()-- 36MB for best edges.
OverlapCache()-- 94MB for tigs.
OverlapCache()-- 25MB for tigs - read layouts.
OverlapCache()-- 36MB for tigs - error profiles.
OverlapCache()-- 6400MB for tigs - error profile overlaps.
OverlapCache()-- 0MB for other processes.
OverlapCache()-- ---------
OverlapCache()-- 6618MB for data structures (sum of above).
OverlapCache()-- ---------
OverlapCache()-- 18MB for overlap store structure.
OverlapCache()-- 18963MB for overlap data.
OverlapCache()-- ---------
OverlapCache()-- 25600MB allowed.
OverlapCache()--
OverlapCache()-- Retain at least 70 overlaps/read, based on 35.48x coverage.
OverlapCache()-- Initial guess at 1301 overlaps/read.
OverlapCache()--
OverlapCache()-- Adjusting for sparse overlaps.
OverlapCache()--
OverlapCache()-- reads loading olaps olaps memory
OverlapCache()-- olaps/read all some loaded free
OverlapCache()-- ---------- ------- ------- ----------- ------- --------
OverlapCache()-- 1301 517418 437225 615422644 12.67% 9572 MB
OverlapCache()-- 2735 529812 424831 1234265368 25.41% 129 MB
OverlapCache()-- 2755 530077 424566 1242759559 25.58% 0 MB
OverlapCache()--
OverlapCache()-- Loading overlaps.
OverlapCache()--
OverlapCache()-- read from store saved in cache
OverlapCache()-- ------------ --------- ------------ ---------
OverlapCache()-- 504456736 (010.39%) 125113686 (002.58%)
OverlapCache()-- 973238122 (020.04%) 245797840 (005.06%)
OverlapCache()-- 1427045622 (029.38%) 363928617 (007.49%)
OverlapCache()-- 1892364969 (038.96%) 484613230 (009.98%)
OverlapCache()-- 2418001048 (049.78%) 613334872 (012.63%)
OverlapCache()-- 3001630838 (061.79%) 750768422 (015.46%)
OverlapCache()-- 3535993019 (072.79%) 882505988 (018.17%)
OverlapCache()-- 4048959685 (083.35%) 1012151317 (020.84%)
OverlapCache()-- 4556016611 (093.79%) 1139890749 (023.47%)
OverlapCache()-- ------------ --------- ------------ ---------
OverlapCache()-- 4857497842 (100.00%) 1212567106 (024.96%)
OverlapCache()--
OverlapCache()-- Ignored 490239518 duplicate overlaps.
OverlapCache()--
OverlapCache()-- Symmetrizing overlaps.
OverlapCache()-- Finding missing twins.
OverlapCache()-- Found 676981120 missing twins in 1212567106 overlaps, 9623 are strong.
OverlapCache()-- Dropping weak non-twin overlaps; allocated 0 MB scratch space.
OverlapCache()-- Dropped 306637017 overlaps; scratch space released.
OverlapCache()-- Adding 370344103 missing twin overlaps.
OverlapCache()-- Finished.
BestOverlapGraph()-- allocating best edges (29MB)
BestOverlapGraph()-- finding initial best edges.
BestOverlapGraph()-- filtering suspicious reads.
BestOverlapGraph()-- marked 363 reads as suspicious.
BestOverlapGraph()-- filtering high error edges.
BestOverlapGraph()-- filtering reads with lopsided best edges.
BestOverlapGraph()-- filtering spur reads.
BestOverlapGraph()-- detected 19367 spur reads and 4185 singleton reads.
BestOverlapGraph()-- removing best edges for contained reads.
==> BUILDING GREEDY TIGS.
breakSingletonTigs()-- Removed 17349 singleton tigs; reads are now unplaced.
optimizePositions()-- Optimizing read positions for 22152 reads in 954644 tigs, with 4 threads.
optimizePositions()-- Allocating scratch space for 954644 reads (0 KB).
optimizePositions()-- Initializing positions with 4 threads.
optimizePositions()-- Recomputing positions, iteration 1, with 4 threads.
optimizePositions()-- Reset zero.
optimizePositions()-- Checking convergence.
optimizePositions()-- converged: 946184 reads
optimizePositions()-- changed: 8460 reads
optimizePositions()-- Recomputing positions, iteration 2, with 4 threads.
optimizePositions()-- Reset zero.
optimizePositions()-- Checking convergence.
optimizePositions()-- converged: 951172 reads
optimizePositions()-- changed: 3472 reads
optimizePositions()-- Recomputing positions, iteration 3, with 4 threads.
optimizePositions()-- Reset zero.
optimizePositions()-- Checking convergence.
optimizePositions()-- converged: 951333 reads
optimizePositions()-- changed: 3311 reads
optimizePositions()-- Recomputing positions, iteration 4, with 4 threads.
optimizePositions()-- Reset zero.
optimizePositions()-- Checking convergence.
optimizePositions()-- converged: 951405 reads
optimizePositions()-- changed: 3239 reads
optimizePositions()-- Recomputing positions, iteration 5, with 4 threads.
optimizePositions()-- Reset zero.
optimizePositions()-- Checking convergence.
optimizePositions()-- converged: 951445 reads
optimizePositions()-- changed: 3199 reads
optimizePositions()-- Expanding short reads with 4 threads.
optimizePositions()-- Updating positions.
optimizePositions()-- Finished.
==> PLACE CONTAINED READS.
computeErrorProfiles()-- Computing error profiles for 22152 tigs, with 4 threads.
computeErrorProfiles()-- Finished.
placeContains()-- placing 880813 contained and 28687 unplaced reads, with 4 threads.
placeContains()-- Placed 623978 contained reads and 1072 unplaced reads.
placeContains()-- Failed to place 256835 contained reads (too high error suspected) and 27615 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 22152 reads in 954644 tigs, with 4 threads.
optimizePositions()-- Allocating scratch space for 954644 reads (0 KB).
optimizePositions()-- Initializing positions with 4 threads.
bogart: bogart/AS_BAT_OptimizePositions.C:140: void Unitig::optimize_initPlace(uint32, optPos*, optPos*, bool, std::set<unsigned int>&, bool): Assertion `cnt > 0' failed.
Failed with 'Aborted'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::102 in _Z17AS_UTL_catchCrashiP7siginfoPv()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
bogart/AS_BAT_OptimizePositions.C::140 in _ZN6Unitig18optimize_initPlaceEjP6optPosS1_bRSt3setIjSt4lessIjESaIjEEb()
bogart/AS_BAT_OptimizePositions.C::391 in _ZN9TigVector17optimizePositionsEPKcS1_._omp_fn.0()
../../../gcc-6.1.0/libgomp/team.c::119 in gomp_thread_start()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
Do you have any idea what could be the problem? Any help is greatly appreciated!
Best Andrin
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