[mira_talk] MIRA Failure - Geneious 8 - Bug report
- From: Zain A Alvi <zain.alvi@xxxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 17 Dec 2014 13:23:59 +0000
Dear Sir or Madam,
I hope this reaches you well. I was trying to run MIRA on Geneious 8.0.4 and it
crashed. I have attached bug report for your kind review. Please let me know
on how to adjust the settings to allow MIRA to work properly on Geneious. I
would really appreciate it.
Sincerely,
Zain
MIRA crashed. This is a bug in MIRA, not Geneious. To report this bug, use the
MIRA bug tracking system at http://sourceforge.net/p/mira-assembler/tickets/
If it is small enough you may want to include a copy of the input data from
C:\Users\Zain_2\Geneious 8.0 Data\temp\43 From temporary directory:
C:\Users\Zain_2\Geneious 8.0 Data\temp\43 Ran command:
C:\ProgramData\Geneious\plugins\com.biomatters.plugins.mira.MiraPlugin\com\biomatters\plugins\mira\windows\bin\mira.exe
manifest.txt The temporary directory will be deleted either next time MIRA is
run or Geneious is restarted. MIRA failed with error code 100 This is MIRA 4.0
. 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. To (un-)subscribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html After subscribing, mail general
questions to the MIRA talk mailing list: mira_talk@xxxxxxxxxxxxx To report
bugs or ask for features, please use the SourceForge ticketing system at:
http://sourceforge.net/p/mira-assembler/tickets/ This ensures that requests do
not get lost. Compiled by: Matt Thu, Feb 13, 2014 10:13:59 PM On:
CYGWIN_NT-6.1 Matt-PC 1.7.28(0.271/5/3) 2014-02-09 21:06 x86_64 Cygwin 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: Looking for files named in data ...Pushing back filename:
"geneious_in_0.fastq" Manifest: projectname: geneious job:
denovo,genome,accurate parameters: -NAG_AND_WARN:check_maxreadnamelength=no
-NAG_AND_WARN:average_coverage_value=80 Manifest load entries: 1 MLE 1: RGID: 1
RGN: group0 SN: StrainX SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0 ST: 2 (IonTor)
namschem: 4 SID: 0 DQ: 20 BB: 0 Rail: 0 CER: 0 geneious_in_0.fastq Parameters
parsed without error, perfect. -CL:pec and -CO:emeas1clpec are set, setting
-CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for: Sanger data Used parameter settings: General
(-GE): Project name : geneious Number of threads (not) : 2 Automatic memory
management (amm) : yes Keep percent memory free (kpmf) : 15 Max. process size
(mps) : 0 EST SNP pipeline step (esps) : 0 Colour reads by hash frequency
(crhf) : yes Load reads options (-LR): Wants quality file (wqf) : [ion] yes
Filecheck only (fo) : no Assembly options (-AS): Number of passes (nop) : 5
Skim each pass (sep) : yes Maximum number of RMB break loops (rbl) : 3 Maximum
contigs per pass (mcpp) : 0 Minimum read length (mrl) : [ion] 40 Minimum reads
per contig (mrpc) : [ion] 5 Enforce presence of qualities (epoq) : [ion] yes
Automatic repeat detection (ard) : yes Coverage threshold (ardct) : [ion] 2
Minimum length (ardml) : [ion] 200 Grace length (ardgl) : [ion] 20 Use uniform
read distribution (urd) : no Start in pass (urdsip) : 4 Cutoff multiplier
(urdcm) : [ion] 1.5 Spoiler detection (sd) : yes Last pass only (sdlpo) : yes
Use genomic pathfinder (ugpf) : yes Use emergency search stop (uess) : yes ESS
partner depth (esspd) : 500 Use emergency blacklist (uebl) : yes Use max.
contig build time (umcbt) : no Build time in seconds (bts) : 10000 Strain and
backbone options (-SB): Bootstrap new backbone (bnb) : yes Start backbone usage
in pass (sbuip) : 3 Backbone rail from strain (brfs) : Backbone rail length
(brl) : 0 Backbone rail overlap (bro) : 0 Trim overhanging reads (tor) : yes
(Also build new contigs (abnc)) : yes Dataprocessing options (-DP): Use read
extensions (ure) : [ion] no Read extension window length (rewl) : [ion] 15 Read
extension w. maxerrors (rewme) : [ion] 2 First extension in pass (feip) : [ion]
0 Last extension in pass (leip) : [ion] 0 Clipping options (-CL): SSAHA2 or
SMALT clipping: Gap size (msvsgs) : [ion] 8 Max front gap (msvsmfg) : [ion] 8
Max end gap (msvsmeg) : [ion] 12 Strict front clip (msvssfc) : [ion] 0 Strict
end clip (msvssec) : [ion] 0 Possible vector leftover clip (pvlc) : [ion] no
maximum len allowed (pvcmla) : [ion] 18 Min qual. threshold for entire read
(mqtfer): [ion] 0 Number of bases (mqtfernob) : [ion] 0 Quality clip (qc) :
[ion] no Minimum quality (qcmq) : [ion] 20 Window length (qcwl) : [ion] 30 Bad
stretch quality clip (bsqc) : [ion] no Minimum quality ... ossible overlaps:
Localtime: Wed Dec 17 01:42:22 2014 Now running threaded and partitioned
skimmer with 36 partitions in 2 threads: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done. truncating
geneious_assembly/geneious_d_tmp/geneious_int_posmatchf_pass.1.bin truncated
geneious_assembly/geneious_d_tmp/geneious_int_posmatchf_pass.1.bin from
1827185736 to 998845104 truncating
geneious_assembly/geneious_d_tmp/geneious_int_posmatchc_pass.1.bin truncated
geneious_assembly/geneious_d_tmp/geneious_int_posmatchc_pass.1.bin from
1763322840 to 939415440 Hits chosen: 161521712 Localtime: Wed Dec 17
02:23:41 2014 Total megahubs: 0 Cutting back possible chimeras ... done.
Chimeras were searched for ... looking for hits to purge. truncating
geneious_assembly/geneious_d_tmp/geneious_int_posmatchf_pass.1.bin from
998845104 to 998666352 truncating
geneious_assembly/geneious_d_tmp/geneious_int_posmatchc_pass.1.bin from
939415440 to 939242568 System memory: 12864950272 Mem2keepfree: 1929742540 Used
by MIRA: 7431847936 Mem avail: 3503359796 rsh increased memtouse to: 3503359796
Edge vector capacity: 114958956 Can load up to 114953956 skim edges at once.
Partitioning into 2 blocks. Blocks: 1700673 2488886 We have 161492410 skims in
file. Localtime: Wed Dec 17 02:24:20 2014 De-normalising SKIM hits ... (this
will take a while) Localtime: Wed Dec 17 02:26:02 2014 Localtime: Wed Dec 17
02:26:26 2014 Writing normalised skimblock 0 ( 3.3 GiB) ... done. Localtime:
Wed Dec 17 02:32:38 2014 Localtime: Wed Dec 17 02:32:48 2014 Writing normalised
skimblock 1700673 ( 1.6 GiB) ... done. Localtime: Wed Dec 17 02:33:25 2014
Loading block 0 Loading 109479959 elements at offset 0 Loaded 109479959
elements Loading block 1 Loading 52012451 elements at offset 3503358688 Loaded
52012451 elements Localtime: Wed Dec 17 02:35:10 2014 Step 0 Loading block 0
Loading 109479959 elements at offset 0 Loaded 109479959 elements Loading block
1 Loading 52012451 elements at offset 3503358688 Loaded 52012451 elements
Localtime: Wed Dec 17 02:38:23 2014 Only long reads Step 10 Loading block 0
Loading 109479959 elements at offset 0 Loaded 109479959 elements Loading block
1 Loading 52012451 elements at offset 3503358688 Loaded 52012451 elements Total
skims taken: 9278894 Step 20 Loading block 0 Loading 109479959 elements at
offset 0 Loaded 109479959 elements Loading block 1 Loading 52012451 elements at
offset 3503358688 Loaded 52012451 elements Total skims taken: 9278894 Step 30
Loading block 0 Loading 109479959 elements at offset 0 Loaded 109479959
elements Loading block 1 Loading 52012451 elements at offset 3503358688 Loaded
52012451 elements Total skims taken: 13066788 Step 40 Loading block 0 Loading
109479959 elements at offset 0 Loaded 109479959 elements Loading block 1
Loading 52012451 elements at offset 3503358688 Loaded 52012451 elements Total
skims taken: 13066788 Step 50 Total skims taken: 13066788 Step 53 Loading block
0 Loading 109479959 elements at offset 0 Loaded 109479959 elements Loading
block 1 Loading 52012451 elements at offset 3503358688 Loaded 52012451 elements
Total skims taken: 25267100 Step 55 Loading block 0 Loading 109479959 elements
at offset 0 Loaded 109479959 elements Loading block 1 Loading 52012451 elements
at offset 3503358688 Loaded 52012451 elements Total skims taken: 25268901 Step
60 Loading block 0 Loading 109479959 elements at offset 0 Loaded 109479959
elements Loading block 1 Loading 52012451 elements at offset 3503358688 Loaded
52012451 elements Total skims taken: 25270781 Step solexa by critlevel
rsh4_takeSolexaByCritLevel. Loading block 0 Loading 109479959 elements at
offset 0 Loaded 109479959 elements Loading block 1 Loading 52012451 elements at
offset 3503358688 Loaded 52012451 elements Taken 0 hits.
rsh4_takeSolexaByCritLevel. Loading block 0 Loading 109479959 elements at
offset 0 Loaded 109479959 elements Loading block 1 Loading 52012451 elements at
offset 3503358688 Loaded 52012451 elements Taken 0 hits. Step template overlaps
Loading block 0 Loading 109479959 elements at offset 0 Loaded 109479959
elements Loading block 1 Loading 52012451 elements at offset 3503358688 Loaded
52012451 elements Step NAO rsh4_takeNeedAllOverlaps. None needed. Total skims
taken: 25270781 Filtering forward skims. Localtime: Wed Dec 17 02:53:23 2014
Writing reduced skim file: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%]
....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%] Done. Done. Filtering complement skims.
Localtime: Wed Dec 17 02:54:43 2014 Writing reduced skim file: [0%] ....|....
[10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|....
[60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Done.
Done all filtering. Failure, wrapped MIRA process aborted.
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