Hello, I am attempting to run a hybrid assembly with long read pacbio data and
iontorrent data. I am getting the following error / log file output:
This is MIRA 4.9.6.
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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Compiled by: bach
Sun May 1 18:46:19 CEST 2016
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 c31a-s1.ufhpc 2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24
10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
Looking for files named in data ...Manifest:
projectname: Mfruct_01
job: genome,denovo,accurate
parameters: -GE:not=10 PCBIOHQ_SETTINGS -CL:pec=yes
Manifest load entries: 2
MLE 1:
RGID: 1
RGN: IonTorrentReads 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
Ion_torrent_LIL-31_Rollins_62.fastq MLE 2:
RGID: 2
RGN: PacBioReads SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 3 (PcBioHQ) namschem: 8 SID: 0
DQ: 20
BB: 0 Rail: 0 CER: 0
Full_PacBio_NS467.subreads.fastq
********************************************************************************
* Binary: /apps/mira/4.9.6/bin/mira *
********************************************************************************
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data, 454 data
Used parameter settings:
General (-GE):
Project name : Mfruct_01
Number of threads (not) : 10
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 kmer frequency (crkf) : yes
Preprocess only (ppo) : no
Load reads options (-LR):
Wants quality file (wqf) : [ion] yes
[pbh] yes
Filecheck only (fo) : no
Assembly options (-AS):
Use genomic pathfinder (ugpf) : yes
Number of passes (nop) : 0
Kmer series (kms) :
Maximum number of RMB break loops (rbl) : 3
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [ion] 40
[pbh] 40
Minimum reads per contig (mrpc) : [ion] 5
[pbh] 5
Enforce presence of qualities (epoq) : [ion] yes
[pbh] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [ion] 2
[pbh] 2
Minimum length (ardml) : [ion] 200
[pbh] 200
Grace length (ardgl) : [ion] 20
[pbh] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [ion] 1.5
[pbh] 1.5
Spoiler detection (sd) : yes
Last pass only (sdlpo) : 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) : [ion] yes
[pbh] 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
Dataprocessing options (-DP):
Use read extensions (ure) : [ion] no
[pbh] no
Read extension window length (rewl) : [ion] 15
[pbh] 15
Read extension w. maxerrors (rewme) : [ion] 2
[pbh] 2
First extension in pass (feip) : [ion] 0
[pbh] 0
Last extension in pass (leip) : [ion] 0
[pbh] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [ion] 8
[pbh] 8
Max front gap (msvsmfg) : [ion] 8
[pbh] 8
Max end gap (msvsmeg) : [ion] 12
[pbh] 12
Strict front clip (msvssfc) : [ion] 0
[pbh] 0
Strict end clip (msvssec) : [ion] 0
[pbh] 0
Possible vector leftover clip (pvlc) : [ion] no
[pbh] no
maximum len allowed (pvcmla) : [ion] 18
[pbh] 18
Min qual. threshold for entire read (mqtfer): [ion] 0
[pbh] 0
Number of bases (mqtfernob) : [ion] 0
[pbh] 0
Quality clip (qc) : [ion] no
[pbh] no
Minimum quality (qcmq) : [ion] 20
[pbh] 20
Window length (qcwl) : [ion] 30
[pbh] 30
Bad stretch quality clip (bsqc) : [ion] no
[pbh] no
Minimum quality (bsqcmq) : [ion] 5
[pbh] 5
Window length (bsqcwl) : [ion] 20
[pbh] 20
Masked bases clip (mbc) : [ion] yes
[pbh] yes
Gap size (mbcgs) : [ion] 5
[pbh] 5
Max front gap (mbcmfg) : [ion] 12
[pbh] 12
Max end gap (mbcmeg) : [ion] 12
[pbh] 12
Lower case clip front (lccf) : [ion] yes
[pbh] yes
Lower case clip back (lccb) : [ion] yes
[pbh] yes
Clip poly A/T at ends (cpat) : [ion] no
[pbh] no
Keep poly-a signal (cpkps) : [ion] no
[pbh] no
Minimum signal length (cpmsl) : [ion] 12
[pbh] 12
Max errors allowed (cpmea) : [ion] 1
[pbh] 1
Max gap from ends (cpmgfe) : [ion] 9
[pbh] 9
Clip 3 prime polybase (c3pp) : [ion] no
[pbh] no
Minimum signal length (c3ppmsl) : [ion] 15
[pbh] 15
Max errors allowed (c3ppmea) : [ion] 3
[pbh] 3
Max gap from ends (c3ppmgfe) : [ion] 9
[pbh] 9
Clip known adaptors right (ckar) : [ion] yes
[pbh] no
Ensure minimum left clip (emlc) : [ion] no
[pbh] no
Minimum left clip req. (mlcr) : [ion] 4
[pbh] 4
Set minimum left clip to (smlc) : [ion] 4
[pbh] 4
Ensure minimum right clip (emrc) : [ion] no
[pbh] no
Minimum right clip req. (mrcr) : [ion] 10
[pbh] 10
Set minimum right clip to (smrc) : [ion] 15
[pbh] 15
GB chimera detection clip (gbcdc) : yes
KMER junk detection (kjd) : yes
KMER junk complete kill (kjck) : no
DEPRECATED! Apply SKIM chimera detection clip (ascdc): yes
DEPRECATED! Apply SKIM junk detection clip (asjdc): no
Propose end clips (pec) : [ion] yes
[pbh] yes
Kmer size (peckms) : 27
Minimum kmer for forward-rev (pmkfr) : 1
Minimum total kmer (pmtk) : 3
Handle Solexa GGCxG problem (pechsgp) : yes
Rare kmer mask (rkm) : [ion] no
[pbh] no
Front freq (pffreq) : [ion] 1
[pbh] 1
Back freq (pbfreq) : [ion] 1
[pbh] 1
Front forward-rev (pffore) : [ion] no
[pbh] no
Back forward-rev (pbfore) : [ion] no
[pbh] no
Front conf. multi-seq type (pfcmst) : [ion] no
[pbh] no
Back conf. multi-seq type (pbcmst) : [ion] no
[pbh] no
Front seen at low pos (pfsalp) : [ion] no
[pbh] no
Back seen at low pos (pbsalp) : [ion] no
[pbh] no
Clip bad solexa ends (cbse) : [ion] no
[pbh] no
Search PhiX174 (spx174) : [ion] no
[pbh] no
Filter PhiX174 (fpx174) : [ion] no
[pbh] no
Filter rRNA (frrna) : no
Pairs (frrnap) : no
Number of kmers (frrnank) : 17
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 10
Also compute reverse complements (acrc) : yes
Kmer size (kms) : 17
Automatic increase per pass (kmsaipp) : 0
Kmer size max(kmsmax) : 0
Kmer save stepping (kss) : 1
Percent required (pr) : [ion] 50
[pbh] 80
Max hits per read (mhpr) : 2000
Filter megahubs (fmh) : yes
Megahub cap (mhc) : 150000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : no
Max kmers in memory (mkim) : 15000000
MemCap: hit reduction (mchr) : 2048
Parameters for Kmer Statistics (-KS):
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) : yes
Nasty repeat ratio (nrr) : 100
Nasty repeat coverage (nrc) : 0
Lossless digital normalisation (ldn) : no
Repeat level in info file (rliif) : 6
Memory to use (mtu) : 75
Rare kmer final kill (rkfk) : 0
Pathfinder options (-PF):
Use quick rule (uqr) : [ion] yes
[pbh] yes
Quick rule min len 1 (qrml1) : [ion] 80
[pbh] 80
Quick rule min sim 1 (qrms1) : [ion] 90
[pbh] 90
Quick rule min len 2 (qrml2) : [ion] 60
[pbh] 60
Quick rule min sim 2 (qrms2) : [ion] 95
[pbh] 95
Backbone quick overlap min len (bqoml) : [ion] 80
[pbh] 80
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [ion] 20
[pbh] 20
Bandwidth max (bmax) : [ion] 80
[pbh] 200
Bandwidth min (bmin) : [ion] 20
[pbh] 20
Minimum score (ms) : [ion] 15
[pbh] 15
Minimum overlap (mo) : [ion] 19
[pbh] 17
Minimum relative score in % (mrs) : [ion] 70
[pbh] 70
Enforce clean ends (ece) : no
Clean end distance (ced) : 0
Clean end mismatch allowed (cema) : 0
Extra gap penalty (egp) : yes
extra gap penalty levels (egpl) : 0,0,100
Max. egp in percent (megpp) : 100
Solexa_hack_max_errors (shme) : [ion] -1
[pbh] -1
Contig parameters (-CO):
Name prefix (np) : Mfruct_01
Reject on drop in relative alignment score in % (rodirs) : [ion] 25
[pbh] 30
CMinimum relative score in % (cmrs) : [ion] -1
[pbh] -1
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [ion] 4
[pbh] 3
Minimum neighbour quality needed for tagging (mnq) : [ion] 20
[pbh] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [ion] 25
[pbh] 25
Minimum coverage percentage (mcp) : 10
End-read Marking Exclusion Area in bases (emea) : [ion] 1
[pbh] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [ion] no
[pbh] no
Also mark gap bases - even multicolumn (amgbemc) : [ion] yes
[pbh] yes
Also mark gap bases - need both strands (amgbnbs): [ion] yes
[pbh] yes
Force non-IUPAC consensus (fnic) : [ion] no
[pbh] no
Merge short reads (msr) : [ion] no
[pbh] no
Max errors (msrme) : [ion] 0
[pbh] 0
Keep ends unmerged (msrkeu) : [ion] -1
[pbh] -1
Gap override ratio (gor) : [ion] 66
[pbh] 66
Edit options (-ED):
GB read editing (gbre) : yes
Mira automatic contig editing (mace) : yes
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [ion] yes
[pbh] 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) : no
Extended log (el) : no
Nag and Warn (-NW):
Check NFS (cnfs) : stop
Check multi pass mapping (cmpm) : stop
Check template problems (ctp) : stop
Check SRA read names (csrn) : 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 : Mfruct_01_assembly
For writing result files : Mfruct_01_assembly/Mfruct_01_d_results
For writing result info files : Mfruct_01_assembly/Mfruct_01_d_info
For writing tmp files : Mfruct_01_assembly/Mfruct_01_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : Mfruct_01_assembly/Mfruct_01_d_chkpt
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [ion] no
[pbh] no
Save tagged singlets in project (stsip) : [ion] yes
[pbh] 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) : no
Saved as simple text format (ort) : no
Saved as wiggle (orw) : yes
Temporary result files:
Saved as CAF (otc) : no
Saved as MAF (otm) : yes
Saved as FASTA (otf) : yes
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 : Mfruct_01_out.caf
MAF : Mfruct_01_out.maf
FASTA : Mfruct_01_out.unpadded.fasta
FASTA quality : Mfruct_01_out.unpadded.fasta.qual
FASTA (padded) : Mfruct_01_out.padded.fasta
FASTA qual.(pad): Mfruct_01_out.padded.fasta.qual
GAP4 (directory): Mfruct_01_out.gap4da
ACE : Mfruct_01_out.ace
HTML : Mfruct_01_out.html
Simple text : Mfruct_01_out.txt
TCS overview : Mfruct_01_out.tcs
Wiggle : Mfruct_01_out.wig
------------------------------------------------------------------------------
Creating directory Mfruct_01_assembly ... done.
Creating directory Mfruct_01_assembly/Mfruct_01_d_results ... done.
Creating directory Mfruct_01_assembly/Mfruct_01_d_info ... done.
Creating directory Mfruct_01_assembly/Mfruct_01_d_chkpt ... done.
Creating directory Mfruct_01_assembly/Mfruct_01_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Wed Jul 5 14:03:32 2017
Loading reads from Ion_torrent_LIL-31_Rollins_62.fastq type fastq
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Loading reads from Full_PacBio_NS467.subreads.fastq type fastq
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
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.
4374899 reads with valid data for assembly.
Localtime: Wed Jul 5 14:04:27 2017
Generated 4374899 unique DNA template ids for 4374899 valid reads.
No useful template information found.
TODO: Like Readpool: strain x has y reads
Have read pool with 4374899 reads.
===========================================================================
Backbones: 0 Backbone rails: 0
Sequencing technology statistics:
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa Solid
------------------------------------------------------------
Total reads 0 0 4086596 288303 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 3922103 288250 0 0 0 0
Avg. tot rlen 0 0 263 6559 0 0 0 0
Avg. used rlen 0 0 273 6561 0 0 0 0
W/o clips 0 0 4086596 288303 0 0 0 0
Readgroup statistics:
RG 1 IonTor avg total len: 263 avg clip len: 273 total bases: 1078210734 used
bases: 1074389929
RG 2 PcBioHQ avg total len: 6559 avg clip len: 6561 total bases: 1891210416
used bases: 1891208450
===========================================================================
Read m170525_p0/6151/0_35037 has 35037 bases (clipped). Too long (>32760
Read m170525_p0/9384/0_33335 has 33335 bases (clipped). Too long (>32760
Read m170525_p0/14486/0_33173 has 33173 bases (clipped). Too long (>32760
Read m170525_p0/14818/0_40684 has 40684 bases (clipped). Too long (>32760
Read m170525_p0/17912/4469_55684 has 51215 bases (clipped). Too long (>32760
Read m170525_p0/20028/0_44817 has 44817 bases (clipped). Too long (>32760
Read m170525_p0/20267/6999_40553 has 33554 bases (clipped). Too long (>32760
Read m170525_p0/25190/0_36044 has 36044 bases (clipped). Too long (>32760
Read m170525_p0/26452/18630_57638 has 39008 bases (clipped). Too long (>32760
Read m170525_p0/28777/0_40109 has 40109 bases (clipped). Too long (>32760
More long reads may exist, but stopping output here.
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 131850364 kB
MemFree: 2387220 kB
Buffers: 0 kB
Cached: 71402884 kB
SwapCached: 0 kB
Active: 56610828 kB
Inactive: 50397892 kB
Active(anon): 36970524 kB
Inactive(anon): 1519052 kB
Active(file): 19640304 kB
Inactive(file): 48878840 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 236 kB
Writeback: 300 kB
AnonPages: 35603920 kB
Mapped: 49076 kB
Shmem: 2883992 kB
Slab: 20125576 kB
SReclaimable: 571312 kB
SUnreclaim: 19554264 kB
KernelStack: 18880 kB
PageTables: 79852 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 131850364 kB
Committed_AS: 44375272 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 1268020 kB
VmallocChunk: 34288874360 kB
HardwareCorrupted: 0 kB
AnonHugePages: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 4096 kB
DirectMap2M: 2019328 kB
DirectMap1G: 132120576 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 30715
Pid: 30715
PPid: 30714
TracerPid: 0
Uid: 10832 10832 10832 10832
Gid: 3092 3092 3092 3092
Utrace: 0
FDSize: 64
Groups: 3092 3155 3171 13002 13006
VmPeak: 25446184 kB
VmSize: 25121984 kB
VmLck: 0 kB
VmHWM: 25235380 kB
VmRSS: 24911828 kB
VmData: 25015436 kB
VmStk: 92 kB
VmExe: 9564 kB
VmLib: 0 kB
VmPTE: 48732 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/513049
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: 000003ff
Cpus_allowed_list: 0-9
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
Mems_allowed_list: 0-1
voluntary_ctxt_switches: 102
nonvoluntary_ctxt_switches: 210
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 4374899 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 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_skimmegahubs: 0 24 B 0 B 0 B
AS_usedtmpfiles: 1 48 B 0 B 0 B
Total: 1008 (1008 B)
================================================================================
Dynamic s allocs: 0
Dynamic m allocs: 0
Align allocs: 0
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* MIRA found 152 very long reads (too long for normal reads), see log above. *
********************************************************************************
->Thrown: void Assembly::basicDataChecks()
->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: /ufrc/barbazuk/rotheconrad/Rollins/Mfruct
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Wrapped MIRA process exited with an error.
###################################################################################
################################END LOG FILE
########################################
###################################################################################
Is there a way to tell MIRA to run with the 152 long reads anyways or do I
really need to filter those out?
If I must filter them, is there a way to get MIRA to tell me all 152 long read
names?
We took extreme care to prepare the DNA for PacBio sequencing in order to get
really long reads so I believe them to be good.
This is my manifest.conf file:
project = Mfruct_01
job = genome,denovo,accurate
parameters = -GE:not=10 PCBIOHQ_SETTINGS -CL:pec=yes
readgroup = IonTorrentReads
data = Ion_torrent_LIL-31_Rollins_62.fastq
technology = iontor
readgroup = PacBioReads
data = Full_PacBio_NS467.subreads.fastq
technology = pcbiohq
And I simply execute it with the command:
mira manifest.conf
I am running on a cluster using the SLURM job scheduler asking for 1 task, 10
cpu per task, and 40 gb memory.
I am a student research assistant at the University of Florida.
Thank you,
Roth Conrad.
