chrishah
The program stops at interation1
I'm just starting with MITObim to get a complete mitochondrial genome from my data.
So far, I've gotten the maf file that seems to be successfully generated by using mira 4.0.2. For example, some reads in the maf file were analyzed by BLAST, and then matched the mitochondrial genome from an animal with the same genus.
Next, I move to MITObim, but it stops at iteration 1. Log says like this;
MITObim - mitochondrial baiting and iterative mapping version 1.9.1 author: Christoph Hahn, (c) 2012-2018
Full command run: omitted
All paramters seem to make sense: startiteration: 1 enditeration: 10 sample: testpool omitted paired: 0 (off=0, on=1) assembly mode: 0 (mapping=0, denovo=1) verbose: 0 (off=0, on=1) split: 0 (off=0, on=1) minimum avg. coverage: 0 (off=0) minimum contig length: 0 (off=0) clean: 0 (off=0, on=1) trim reads: 0 (off=0, on=1) trim overhang: 0 (no=0, yes=1) platform: solexa kmer baiting: 31 number of mismatches in mapping assembly: default (15% of average read length loaded) proofreading: off
Starting MITObim
============== ITERATION 1
Oct 27 19:28:18 recover backbone by running miraconvert on maf file fishing readpool using mirabait (k = 31) -f is not a valid from type! your readpool does not contain any reads with reasonable match (k = 31) to your reference - Maybe you ll want to try different settings or even a different reference?
I tried to reduce k-mer some times, but the same log was generated. Could you teach me what is wrong? Thank you very much for your time!
Dear @kataksk,
I suspect that you have some error in your command - note the message about '-f is not a valid from type' above. Hard to say without seeing the actual command though.. Can you please show me the command you ran? Just use dummies for the filenames and -locations if you don't want to disclose the original command to everybody - or send me an email directly - contact details on the main MITObim page. Thanks!
cheers, Christoph
Dear Christoph,
I got almost the same message, but I run the --quick option. I got this message:
**Oct 16 02:59:50
quick option baits reads from provided reference in iteration 0
fishing readpool using mirabait (k = 31)
your readpool does not contain any reads with reasonable match (k = 31) to your reference - Maybe you ll want to try different settings or even a different reference?**
What should I do to correct this error?
thanks in advance for your help
Cheers,
Rubén
