[mira_talk] 454 read mapping problem
- From: Cécile Gracianne <cecile.gracianne@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 31 May 2014 15:17:16 -0400
Hello everyone,
I am running a mapping running with 454 reads on 11 sequences of reference.
I am using mira 4.0.2 on mac.
Mira reads the data file and the manifest but stop before to start the
mapping. I have no idea why.
Here the manifest parameters :
project=mappingIRC04
job=mapping,genome,accurate
readgroup
is_reference
data=References_consensusHsHb2.fasta
strain=SeqRef
readgroup=IRC04HsHb
data=IRC04_renomme_propre.fastq
technology=454
strain=IRC04
The log is pasted below.
Thank in advance for any help!
Cecile
This is MIRA 4.0.2_0+g29f87d4 .
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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To report bugs or ask for features, please use the SourceForge ticketing
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This ensures that requests do not get lost.
Compiled by: bach
Fri Apr 18 14:57:56 CEST 2014
On: Darwin airfau2.fritz.box 13.1.0 Darwin Kernel Version 13.1.0: Thu Jan
16 19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64 x86_64
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: Darwin Yeti.local 12.5.0 Darwin Kernel Version 12.5.0: Sun
Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64
Looking for files named in data ...Pushing back filename:
"References_consensusHsHb2.fasta"
Pushing back filename: "IRC04_renomme_propre.fastq"
Manifest:
projectname: mappingIRC04
job: mapping,genome,accurate
parameters:
Manifest load entries: 2
MLE 1:
RGID: 1
RGN: SN: SeqRef
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 5 (Text) namschem: 6 SID: 0
DQ: 30
BB: 1 Rail: 0 CER: 0
References_consensusHsHb2.fasta MLE 2:
RGID: 2
RGN: IRC04HsHb SN: IRC04
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 1 (454) namschem: 4 SID: 0
DQ: 20
BB: 0 Rail: 0 CER: 0
IRC04_renomme_propre.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 : mappingIRC04
Number of threads (not) : 12
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) : [454] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 1
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 1
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [454] 40
Minimum reads per contig (mrpc) : [454] 5
Enforce presence of qualities (epoq) : [454] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [454] 2
Minimum length (ardml) : [454] 200
Grace length (ardgl) : [454] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [454] 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) : 0
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)) : no
Dataprocessing options (-DP):
Use read extensions (ure) : [454] no
Read extension window length (rewl) : [454] 15
Read extension w. maxerrors (rewme) : [454] 2
First extension in pass (feip) : [454] 0
Last extension in pass (leip) : [454] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [454] 8
Max front gap (msvsmfg) : [454] 8
Max end gap (msvsmeg) : [454] 12
Strict front clip (msvssfc) : [454] 0
Strict end clip (msvssec) : [454] 0
Possible vector leftover clip (pvlc) : [454] no
maximum len allowed (pvcmla) : [454] 18
Min qual. threshold for entire read (mqtfer): [454] 0
Number of bases (mqtfernob) : [454] 0
Quality clip (qc) : [454] no
Minimum quality (qcmq) : [454] 20
Window length (qcwl) : [454] 30
Bad stretch quality clip (bsqc) : [454] no
Minimum quality (bsqcmq) : [454] 5
Window length (bsqcwl) : [454] 20
Masked bases clip (mbc) : [454] yes
Gap size (mbcgs) : [454] 5
Max front gap (mbcmfg) : [454] 12
Max end gap (mbcmeg) : [454] 12
Lower case clip front (lccf) : [454] yes
Lower case clip back (lccb) : [454] yes
Clip poly A/T at ends (cpat) : [454] no
Keep poly-a signal (cpkps) : [454] no
Minimum signal length (cpmsl) : [454] 12
Max errors allowed (cpmea) : [454] 1
Max gap from ends (cpmgfe) : [454] 9
Clip 3 prime polybase (c3pp) : [454] no
Minimum signal length (c3ppmsl) : [454] 15
Max errors allowed (c3ppmea) : [454] 3
Max gap from ends (c3ppmgfe) : [454] 9
Clip known adaptors right (ckar) : [454] yes
Ensure minimum left clip (emlc) : [454] no
Minimum left clip req. (mlcr) : [454] 4
Set minimum left clip to (smlc) : [454] 4
Ensure minimum right clip (emrc) : [454] no
Minimum right clip req. (mrcr) : [454] 10
Set minimum right clip to (smrc) : [454] 15
Apply SKIM chimera detection clip (ascdc) : no
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : [454] yes
Bases per hash (pecbph) : 27
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [454] 1
Back freq (pbfreq) : [454] 1
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [454] no
Back forward-rev (pbfore) : [454] yes
Front conf. multi-seq type (pfcmst) : [454] no
Back conf. multi-seq type (pbcmst) : [454] yes
Front seen at low pos (pfsalp) : [454] no
Back seen at low pos (pbsalp) : [454] no
Clip bad solexa ends (cbse) : [454] no
Search PhiX174 (spx174) : [454] no
Filter PhiX174 (fpx174) : [454] no
Rare kmer mask (rkm) : [454] 0
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 12
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 16
Automatic increase per pass (bphaipp) : 1
Automatic incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 4
Percent required (pr) : [454] 80
Max hits per read (mhpr) : 1000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : yes
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048
Parameters for Hash Statistics (-HS):
Freq. cov. estim. min (fcem) : 0
Freq. estim. min normal (fenn) : 0.4
Freq. estim. max normal (fexn) : 1.6
Freq. estim. repeat (fer) : 1.9
Freq. estim. heavy repeat (fehr) : 8
Freq. estim. crazy (fecr) : 20
Mask nasty repeats (mnr) : no
Nasty repeat ratio (nrr) : 100
Nasty repeat coverage (nrc) : 0
Lossless digital normalisation (ldn) : no
Repeat level in info file (rliif) : 6
Million hashes per buffer (mhpb) : 16
Rare kmer early kill (rkek) : no
Pathfinder options (-PF):
Use quick rule (uqr) : [454] yes
Quick rule min len 1 (qrml1) : [454] 80
Quick rule min sim 1 (qrms1) : [454] 90
Quick rule min len 2 (qrml2) : [454] 60
Quick rule min sim 2 (qrms2) : [454] 95
Backbone quick overlap min len (bqoml) : [454] 80
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [454] 20
Bandwidth max (bmax) : [454] 80
Bandwidth min (bmin) : [454] 20
Minimum score (ms) : [454] 15
Minimum overlap (mo) : [454] 20
Minimum relative score in % (mrs) : [454] 70
Solexa_hack_max_errors (shme) : [454] -1
Extra gap penalty (egp) : [454] no
extra gap penalty level (egpl) : [454] reject_codongaps
Max. egp in percent (megpp) : [454] 100
Contig parameters (-CO):
Name prefix (np) : mappingIRC04
Reject on drop in relative alignment score in % (rodirs) : [454] 30
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [454] 4
Minimum neighbour quality needed for tagging (mnq) : [454] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [454] 25
End-read Marking Exclusion Area in bases (emea) : [454] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [454] no
Also mark gap bases - even multicolumn (amgbemc) : [454] yes
Also mark gap bases - need both strands (amgbnbs): [454] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [454] no
Merge short reads (msr) : [454] no
Max errors (msrme) : [454] 0
Keep ends unmerged (msrkeu) : [454] -1
Gap override ratio (gor) : [454] 66
Edit options (-ED):
Mira automatic contig editing (mace) : yes
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [454] yes
Misc (-MI):
Large contig size (lcs) : 500
Large contig size for stats (lcs4s) : 5000
I know what I do (ikwid) : no
Extra flag 1 / sanity track check (ef1) : no
Extra flag 2 / dnredreadsatpeaks (ef2) : yes
Extra flag 3 / pelibdisassemble (ef3) : yes
Extended log (el) : no
Nag and Warn (-NW):
Check NFS (cnfs) : stop
Check multi pass mapping (cmpm) : stop
Check template problems (ctp) : stop
Check duplicate read names (cdrn) : stop
Check max read name length (cmrnl) : stop
Max read name length (mrnl) : 40
Check average coverage (cac) : stop
Average coverage value (acv) : 80
Directories (-DI):
Top directory for writing files : mappingIRC04_assembly
For writing result files :
mappingIRC04_assembly/mappingIRC04_d_results
For writing result info files :
mappingIRC04_assembly/mappingIRC04_d_info
For writing tmp files : mappingIRC04_assembly/mappingIRC04_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files :
mappingIRC04_assembly/mappingIRC04_d_chkpt
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [454] no
Save tagged singlets in project (stsip) : [454] yes
Remove rollover tmps (rrot) : yes
Remove tmp directory (rtd) : no
Result files:
Saved as CAF (orc) : yes
Saved as MAF (orm) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : no
Saved as GFF3 (org3) : no
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : no
Saved as wiggle (orw) : yes
Temporary result files:
Saved as CAF (otc) : yes
Saved as MAF (otm) : no
Saved as FASTA (otf) : no
Saved as GAP4 (directed assembly) (otg) : no
Saved as phrap ACE (ota) : no
Saved as HTML (oth) : no
Saved as Transposed Contig Summary (ots) : no
Saved as simple text format (ott) : no
Extended temporary result files:
Saved as CAF (oetc) : no
Saved as FASTA (oetf) : no
Saved as GAP4 (directed assembly) (oetg) : no
Saved as phrap ACE (oeta) : no
Saved as HTML (oeth) : no
Save also singlets (oetas) : no
Alignment output customisation:
TEXT characters per line (tcpl) : 60
HTML characters per line (hcpl) : 60
TEXT end gap fill character (tegfc) :
HTML end gap fill character (hegfc) :
File / directory output names:
CAF : mappingIRC04_out.caf
MAF : mappingIRC04_out.maf
FASTA : mappingIRC04_out.unpadded.fasta
FASTA quality : mappingIRC04_out.unpadded.fasta.qual
FASTA (padded) : mappingIRC04_out.padded.fasta
FASTA qual.(pad): mappingIRC04_out.padded.fasta.qual
GAP4 (directory): mappingIRC04_out.gap4da
ACE : mappingIRC04_out.ace
HTML : mappingIRC04_out.html
Simple text : mappingIRC04_out.txt
TCS overview : mappingIRC04_out.tcs
Wiggle : mappingIRC04_out.wig
------------------------------------------------------------------------------
Creating directory mappingIRC04_assembly ... done.
Creating directory mappingIRC04_assembly/mappingIRC04_d_results ... done.
Creating directory mappingIRC04_assembly/mappingIRC04_d_info ... done.
Creating directory mappingIRC04_assembly/mappingIRC04_d_chkpt ... done.
Creating directory mappingIRC04_assembly/mappingIRC04_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Sat May 31 14:26:48 2014
Loading reference backbone from References_consensusHsHb2.fasta type fasta
Localtime: Sat May 31 14:26:48 2014
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Sat May 31 14:26:48 2014
rnm size: 0
Loading quality data from FASTA quality file
References_consensusHsHb2.fasta.qual:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Sat May 31 14:26:48 2014
Done.
Loaded 11 reads with 11 reads having quality accounted for.
Loading reads from IRC04_renomme_propre.fastq type fastq
Localtime: Sat May 31 14:26:48 2014
Loading data from FASTQ file: IRC04_renomme_propre.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 78878 reads, Localtime: Sat May 31 14:26:49 2014
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Deleting gap columns in backbones ... Postprocessing backbone(s) ... this
may take a while.
11 to process
PENG2_d_Hs_rep_c45_bb 361
Contig PENG2_d_Hs_rep_c45_bb has strain SeqRef
CoI_Hb_c175_bb 446
Contig CoI_Hb_c175_bb has strain SeqRef
CoII_Hs_c4_bb 334
Contig CoII_Hs_c4_bb has strain SeqRef
PENG2_a1_Hs_rep_c47_bb 386
Contig PENG2_a1_Hs_rep_c47_bb has strain SeqRef
PENG1_Hb_rep_c154_bb 412
Contig PENG1_Hb_rep_c154_bb has strain SeqRef
PENG1_b_Hs_rep_c156_bb 239
Contig PENG1_b_Hs_rep_c156_bb has strain SeqRef
CLE2_a_Hb_rep_c24_bb 403
Contig CLE2_a_Hb_rep_c24_bb has strain SeqRef
AD_Hb_rep_c31_bb 372
Contig AD_Hb_rep_c31_bb has strain SeqRef
CM2_Hb_rep_c92_bb 412
Contig CM2_Hb_rep_c92_bb has strain SeqRef
VAP2_Hb_rep_c30_bb 379
Contig VAP2_Hb_rep_c30_bb has strain SeqRef
ENG2_Hs_rep_c148_bb 409
Contig ENG2_Hs_rep_c148_bb has strain SeqRef
TODO: Like Readpool: strain x has y reads
Checking reads for trace data (loading qualities if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
No SCF data present in any read, EdIt automatic contig editing for Sanger
data is now switched off.
78889 reads with valid data for assembly.
Localtime: Sat May 31 14:26:49 2014
Generated 78889 unique DNA template ids for 78889 valid reads.
No useful template information found.
TODO: Like Readpool: strain x has y reads
Have read pool with 78889 reads.
===========================================================================
Pool statistics:
Backbones: 11 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 78878 0 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 78867 0 0 0 0 0 0
Avg tot rlen 0 333 0 0 0 0 0 0
Avg rlen used 0 333 0 0 0 0 0 0
W/o clips 0 78878 0 0 0 0 0 0
454 total bases: 26305032 used bases in used reads: 26304650
===========================================================================
Checking pairs of readgroup 1 (named: ''): found 0
Checking pairs of readgroup 2 (named: 'IRC04HsHb'): found 0
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t0.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t1.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t2.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t3.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t4.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t5.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t6.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t7.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t8.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t9.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t10.0.txt
mappingIRC04_assembly/mappingIRC04_d_tmp/mappingIRC04_int_clippings_t11.0.txt
Post-load clips:
Localtime: Sat May 31 14:26:49 2014
Writing temporary hstat files:
freemem: 53494411264
TNH: 5356
XME 1: 0.000212828
XME 2: 0.1
NEPB 1: 104857
NEPB 2: 104857
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Localtime: Sat May 31 14:26:49 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Sat May 31 14:26:49 2014
clean up temporary stat files...Localtime: Sat May 31 14:26:49 2014
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Sat May 31 14:26:49 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
===========================================================================
Pool statistics:
Backbones: 11 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 78878 0 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 0 0
Avg tot rlen 0 333 0 0 0 0 0 0
Avg rlen used 0 0 0 0 0 0 0 0
W/o clips 0 0 0 0 0 0 0 0
454 total bases: 26305032 used bases in used reads: 0
===========================================================================
In func: void Assembly::addRailsToBackbones()
Throw message: No read with sequence length >0 present? Did you provide
data to load?
========================== Memory self assessment
==============================
Running in 64 bit mode.
Could not read file /proc/meminfo
--------------------------------------------------------------------------------
Could not read file /proc/self/status
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 78889 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 11 contigs.
Mem used for reads: 192 (192 B)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 0 24 B 0 B 0 B
AS_skim_edges: 0 24 B 0 B 0 B
AS_adsfacts: 0 24 B 0 B 0 B
AS_confirmed_edges: 0 24 B 0 B 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: 0 24 B 0 B 0 B
AS_clipright: 0 24 B 0 B 0 B
AS_used_ids: 0 24 B 0 B 0 B
AS_multicopies: 0 24 B 0 B 0 B
AS_hasmcoverlaps: 0 24 B 0 B 0 B
AS_maxcoveragereached: 0 24 B 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 0 24 B 0 B 0 B
AS_isdebris: 0 24 B 0 B 0 B
AS_needalloverlaps: 0 24 B 0 B 0 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: 0 40 B 0 B 0 B
AS_skimstaken: 0 40 B 0 B 0 B
AS_numskimoverlaps: 0 24 B 0 B 0 B
AS_numleftextendskims: 0 24 B 0 B 0 B
AS_rightextendskims: 0 24 B 0 B 0 B
AS_skimleftextendratio: 0 24 B 0 B 0 B
AS_skimrightextendratio: 0 24 B 0 B 0 B
AS_usedtmpfiles: 13 432 B 0 B 0 B
Total: 1368 (1 KiB)
================================================================================
Dynamic s allocs: 0
Dynamic m allocs: 0
Align allocs: 0
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* No read with sequence length >0 present? Did you provide data to load?
*
********************************************************************************
->Thrown: void Assembly::addRailsToBackbones()
->Caught: main
Aborting process, probably due to error in the input data or
parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /Applications/mira_4.0.2_darwin13.1.0_x86_64_static/bin
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, wrapped MIRA process aborted.
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