Bugs for MITObim?

[cliu6688]

Dear Christoph:

I am testing MITObim using the testdata1.tgz and run into several problems.

My operating system run centos 6.3. Mira was installed using conda, the version is 4.9.6 The version of MITObim is 1.9.1.

Mira runs fine. However, when I run MITObim.pl, the error message I am getting is:
recover backbone by running miraconvert on maf file

ConvPro::checkTypes: Unknown or illegal file type 'tmp' defined as

miraconvert -f maf -t fasta -A "SOLEXA_SETTINGS -CO:fnicpst=yes" /tmp/tt01/initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf tmp

Details are provided in logfile1.txt

I then switch to the --quick mode. It says "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?"

Details are provided in logfile2.txt

I can try other files. However, considering these are the tutorial files, it has to work first. Please let me know where I did wrong.

Thanks

Chang
logfile1.txt
logfile2.txt