[mira_talk] Crash: "Would extend memory of AS_skim_edges? Shouldn't be. "
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Oct 2012 17:45:08 -0400
Hi Bastien,
I hope you find this bug report useful. We are running mira 3.9.4 on a Dell
R910 server (Centos, IIRC) with 1 TB RAM, 64 cores, 10 TB disk space, and no
NFS disks.
One of my students reported a crash while assembling a 5 mb prokaryote genome.
I got him to repeat it and the same thing happened. I have snipped some of the
'head' and 'tail' of the assembly log, and can make the log available to email
back-channel (It's only 27 K). I have also attached the manifest file. The
log and checkpoint directories are intact - I can zip them up and put them on a
shared dropbox folder if needed.
The student has successfully assembled about 25 other bacterial genomes with
mira, so he pretty much knows his way around the process, therefore I would
discount user error. At the time, we had plenty of RAM and processors free as
we limit our jobs to avoid clogging the beast. We run a bit of a mira factory
so we are aware of clogging up our computer with mira jobs. Usually we only run
2-3 mira jobs at a time on that server. So hopefully running too many mira
jobs is not the cause of the crash.
I'll also get him to repeat the assembly with one processor, as I recall
something like this from the recent past - is this your elusive randomly
occuring SKIM bug?
cheers,
John
<---- manifest
# Manifest file: Bergen_mirahybrid.manifest
project = Bergen_mirahybrid
job = genome, denovo, accurate
parameters = COMMON_SETTINGS -GE:kpmf=15:not=10 -MI:somrnl=0
parameters = 454_SETTINGS -ED:ace=1
readgroup = Bergen-454Reads
data = Bergen_mirahybrid_in.454.fastq
technology = 454
<---- head from the log
This is MIRA 3.9.4 ().
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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http://www.chevreux.org/mira_mailinglists.html
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Compiled by: bach
Sat Aug 25 23:15:51 CEST 2012
On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012
x86_64
GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux nyx 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29
UTC 20
12 x86_64 x86_64 x86_64 GNU/Linux
k: project
v: Bergen_mirahybrid
k: job
v: genome, denovo, accurate
k: parameters
v: COMMON_SETTINGS -GE:kpmf=15:not=10 -MI:somrnl=0
k: parameters
v: 454_SETTINGS -ED:ace=1
k: readgroup
v: Bergen-454Reads
k: data
v: Bergen_mirahybrid_in.454.fastq
k: technology
v: 454
<---- tail of the log.
Mem used for reads: 184 (184 B)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 1855 7 KiB 0 B 4 B
AS_skim_edges: 1872 59 KiB 32 B 0 B
AS_adsfacts: 0 14 KiB 14 KiB 4 B
AS_confirmed_edges: 0 28 KiB 28 KiB 0 B
AS_permanent_overlap_bans: 1 24 B 0 B 0 B
AS_readhitmiss: 0 24 B 0 B 0 B
AS_readhmcovered: 0 24 B 0 B 0 B
AS_count_rhm: 0 24 B 0 B 0 B
AS_clipleft: 1855 7 KiB 0 B 4 B
AS_clipright: 1855 7 KiB 0 B 4 B
AS_used_ids: 0 2 KiB 2 KiB 1 B
AS_multicopies: 1855 2 KiB 0 B 1 B
AS_hasmcoverlaps: 0 2 KiB 2 KiB 1 B
AS_maxcoveragereached: 1855 7 KiB 0 B 4 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 1855 2 KiB 0 B 1 B
AS_isdebris: 1855 2 KiB 0 B 1 B
AS_needalloverlaps: 1855 2 KiB 0 B 1 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 24 B 0 B 0 B
AS_probablermbsnotok: 0 24 B 0 B 0 B
AS_weakrmbsnotok: 0 24 B 0 B 0 B
AS_readmaytakeskim: 1855 2 KiB 1 B 0 B
AS_skimstaken: 1920 2 KiB 0 B 0 B
AS_numskimoverlaps: 1855 7 KiB 0 B 4 B
AS_numleftextendskims: 1855 7 KiB 0 B 4 B
AS_rightextendskims: 1855 7 KiB 0 B 4 B
AS_skimleftextendratio: 1855 2 KiB 0 B 1 B
AS_skimrightextendratio: 1855 2 KiB 0 B 1 B
AS_usedtmpfiles: 45 1 KiB 0 B 0 B
Total: 175816 (172 KiB)
================================================================================
Dynamic allocs: 22
Align allocs: 22
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"Would extend memory of AS_skim_edges? Shouldn't be. File:
Bergen_mirahybrid_assembly
/Bergen_mirahybrid_d_tmp/Bergen_mirahybrid_int_posmatchc_pass.4.bin Line:
348
SE: 295 1845 -18 1770000 959 d1 -1 d2 1 sr 100 sg 0
wg 0
baf 0 nrp 0 rep 1
"
->Thrown: uint32 Assembly::rsh4_loadSkimHitBlock(const string & filename, int32
block
startid, int32 blockendid, int8 rid1dir, int8 rid2dir)
->Caught: main
Aborting process, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/apps/trac/mira-assembler/
and also give a short notice on the mira talk mailing list.
If reporting, please do not delete the log and checkpoint directories, there may
be files in them which could be needed to find the problem.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_tal
k
CWD: /store/home/bkogan/Bergen/ST350/Rawdata/454
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
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