Mitobim-Any one used?- iteration problem

[bioman1]

I am trying to use MITObim for mitchondrial genome assembly project. I have tried tutorial provided in MITObim:https://github.com/chrishah/MITObim

I have installed Mira 3.4.1.1 and MITObim 1.6. Mapping assembly with MIRA 3.4.1.1 was sucessful, however wrapper script MITObim 1.6 stops at iteration 1, it should iterate upto 8 according the the tutorial, it says error "mirabait seems to have failed". What will be the reason

mapping assembly with MIRA 3.4.1.1:
mira --project=initial-mapping-testpool-to-Salpinus-mt --job=mapping,genome,accurate,solexa -MI:somrnl=0 -AS:nop=1 -SB:bft=fasta:bbq=30:bsn=Salpinus-mt-genome SOLEXA_SETTINGS -CO:msr=no -SB:dsn=testpool

for MITObim 1.6:
MITObim.pl -start 1 -end 10 -strain testpool -ref Salpinus_mt_genome -readpool initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf &> log

below is the log file:

MITObim - mitochondrial baiting and iterative mapping
version 1.6
author: Christoph Hahn, (c) 2012-2013


Full command run: ../MITObim_1.6.pl -start 1 -end 10 -strain testpool -ref Salpinus_mt_genome -readpool initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf

All paramters seem to make sense:
startiteration: 1
enditeration: 10
strainname: testpool
refname: Salpinus_mt_genome
readpool: /PATH/MITObim-master/testdata1/initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq
maf: /PATH/Downloads/MITObim-master/testdata1/initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf
quick: 0
paired: 0
denovo: 0 (mapping=0, denovo=1)
noshow: 0
read trimming: 0 (off=0, on=1)
kmer baiting: 31
platform: SOLEXA
clean: 0 (off=0, on=1)
proofread: 0

Starting MITObim

==============
ITERATION 1
==============
May 8 10:20:53


recover backbone by running convert_project on maf file


Parsing special MIRA parameters: SOLEXA_SETTINGS -CO:fnicpst=yes

Ok.
Loading from maf, saving to: fasta fastaqual
First counting reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Now loading and processing data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.Localtime: Thu May 8 10:20:53 2014

Generated 1692 unique template ids for 2548 valid reads.
Localtime: Thu May 8 10:20:53 2014

Seeing strain 1: "testpool"
Seeing strain 2: "Salpinus-mt-genome"
Generated 2 unique strain ids for 2548 reads.
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
... [100%]

Data conversion process finished, no obvious errors encountered.
SC Read:: read name issorted (1) capacity 4294967295(4) size 1
SC Read:: scf path name issorted (1) capacity 255(1) size 1
SC Read:: exp path name issorted (1) capacity 255(1) size 1
SC Read:: machine type issorted (1) capacity 255(1) size 1
SC Read:: primer issorted (1) capacity 255(1) size 1
SC Read:: strain issorted (1) capacity 255(1) size 3
SC Read:: base caller issorted (1) capacity 255(1) size 1
SC Read:: dye issorted (1) capacity 255(1) size 1
SC Read:: process status issorted (1) capacity 255(1) size 1
SC Read:: clone vector name issorted (1) capacity 65535(2) size 1
SC Read:: sequencing vector name issorted (1) capacity 65535(2) size 1
SC asped issorted (1) capacity 4294967295(4) size 1


fishing readpool using mirabait (k = 31)



mirabait seems to have failed - see detailed output above

[maubp]

See also this thread: http://seqanswers.com/forums/showthread.php?t=43064

I suggest you email the authors or the mira_talk mailing list, and include links to these threads.