Can't exec "mirabait": Permission denied

[desmodus1984]

Hi,

I am trying to assemble a genome and I have tried using the docker or the local installation and both times it failed.
I installed MitoBim and put the MIRA bins in the MitoBim folder.
I used the following code:

./MITObim.pl -end 15 -quick /users/PHS0338/jpac1984/data/myse_mito.fasta -sample MYSE-PA113 -ref Myse -readpool /fs/scratch/PHS0338/appz/musket-1.1/BGI-liBZ.0

I got the following report:

MITObim - mitochondrial baiting and iterative mapping
version 1.9.1
author: Christoph Hahn, (c) 2012-2018
quick option selected! -maf option will be ignored (if given)
Full command run:
./MITObim.pl -end 15 -quick /users/PHS0338/jpac1984/data/myse_mito.fasta -sample MYSE-PA113 -ref Myse -readpool /fs/scratch/PHS0338/appz/musket-1.1/BGI-liBZ.0
All paramters seem to make sense:
startiteration: 0
enditeration: 15
sample: MYSE-PA113
refname: Myse
readpool: /fs/scratch/PHS0338/appz/musket-1.1/BGI-liBZ.0
maf: 0
quick: /users/PHS0338/jpac1984/data/myse_mito.fasta
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 0

Mar 22 01:54:11
quick option baits reads from provided reference in iteration 0
fishing readpool using mirabait (k = 31)
Can't exec "mirabait": Permission denied at ./MITObim.pl line 286.
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?

Line 286 is:
@output = qx($mirabait -k $k_bait -n 1 baitfile.fasta $readpool $strainname-readpool-it$currentiteration);
and I have the bins in the PATH, I even used the mirapath option and it failed with an error for the path despite I used the absolute path for the MIRA bins.

---

Then, I tried using the docker, with the following code, and it didn't work too.

WORKING_DIR=/fs/scratch/PHS0338/appz/
singularity run mitobim_latest.sif -i -t -v $WORKING_DIR/:/home/data chrishah/mitobim /bin/bash MITObim.pl -end 10 -quick /users/PHS0338/jpac1984/data/myse_mito.fasta -sample MYSE-PA113 -ref Myse -readpool /fs/scratch/PHS0338/appz/musket-1.1/BGI-liBZ.0

And I got the following error:
set: invalid option: "-i"
FATAL: "-i": executable file not found in $PATH

I would really appreciate your help to troubleshoot what I am doing wrong.

Thanks;

[amantaray]

I had to enable execute permissions on the 'MITObim.pl', 'mira', 'mirabait', 'miramem', and 'miraconvert' files. To do this I ran chmod +x 'file name', as in chmod +x MITObim.pl, for each of the above files which changed their permissions (files turned grey to green in the command line). This bypassed the permission denied error!

However, I then received the following error: mirabait: loadlocale.c:130: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.

To bypass this I ran LC_ALL=C before my code, as mentioned in a previous thread, and afterwards MITObim ran successfully!