I am trying to run a local instance of MapMi (to look at miRNA orthology). I have the program installed on my desktop and am trying to make an initial run with the default configuration file and data included in the program.
$: perl MapMi-MainPipeline-v150b01.pl
+++ Welcome to MapMi - Version 1.5.0.01 - 12032012 +++
+++ Copyright(C) 2009-2012 RNA Genomics Lab@EMBL-EBI +++
+++ Running Job 302141359126851 +++
+++ Cleaning Likely Repeat Sequences +++
.................. and then the program runs through a few steps and fails saying ...
--- FATAL ERROR: There was a problem when running Bowtie for Drosophila_melanogaster. Please doublecheck the situation and try again.
Logfile Had:
sh: 1: HelperPrograms/bowtie: not found
So the way the MapMi works, it has several "helper programs" in their subdirectory within the MapMi directory. These include bowtie, bowtie-build and a few others. Looking at the main perl script, the MapMi program is trying to call these "helper programs" but failing. In the case of bowtie and bowtie-build, I have the programs in my path already. I can alter the MapMi perl script to call them from my bin, and things work fine. I am hesitant to do this for many reasons...one being reproduciblity.
Any clue what I need to do to allow this perl script to call up it's helper programs from the designed helper program folder.
A few other observations: I can ls the helper program folder see that I have executable permissions on each as well as the HelperPrograms directory (.).
$> ls -lha
total 1.2M
drwxr-xr-x 2 neal neal 4.0K Feb 20 2010 .
drwxr-xr-x 5 neal neal 4.0K Jan 25 09:04 ..
-rwxr-xr-x 1 neal neal 758K Feb 20 2010 bowtie
-rwxr-xr-x 1 neal neal 338K Feb 20 2010 bowtie-build
-rwxr-xr-x 1 neal neal 12K Feb 20 2010 dust2
-rwxr-xr-x 1 neal neal 12K Feb 20 2010 dust3
-rwxr-xr-x 1 neal neal 70K Feb 20 2010 fastareformat
However if I try to call a program straight from the command line it fails:
$: ./HelperPrograms/bowtie
bash: ./HelperPrograms/bowtie: No such file or directory
Finally to show that bowtie is correctly installed in my path:
$>ls
dme_mature.fa HelperPrograms-MacOSX.tar.bz2 README.pdf
dme_mature.fa.dusted MapMi-MainPipeline-v150b01.pl Results
HelperPrograms PipelineConfig.conf
HelperPrograms-Linux.tar RawData
(Showing botwtie is not in the current directory)
$> bowtie -h
No index, query, or output file specified!
Usage:
bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]
<m1> Comma-separated list of files containing upstream mates (or the
sequences themselves, if -c is set) paired with mates in <m2>
I can find nothing about this error in the manual/readme. I am sure I am doing something obviously wrong, but can't quite figure it out.
Any direction is greatly appreciated.
Neal
