[andpet]

maq getting started

Ahhh,

sorry but I usually don't work with Macs so I can't really help you. However I have some thoughts about your last error message:

It seems that you are trying to compile a 64bit version of maq by linking a 32bit library which can't work. You could try two things:

1)
make clean
set the environment variable CC to "gcc -m32" (I assume gcc is your compiler)
./configure
make

2)
make clean
edit the file Makefile.generic and look for CFLAGS; change -m64 into -m32
make -f Makefile.generic


Hmm, I don't know if that really helps you. You could also ask the author of maq for a compiled binary for your Mac.

Maybe one of the other mac users in this forum can help you out ...

Wish you luck ,

Andreas

[alig]

To Andreas,

actually you did help me, so thank you, thank you.

you are quite correct that I was trying to compile a 64bit version of maq by linking a 32bit library.

Editing the Makefile.generic at CFLAGS did solve the problem.

I now just have to find some example data to trial the program with while I wait for our sequence to come.

thanks very much again

alig

[vibhavashukla]

easy run failed

hi while running maq-0.6.8 in easy run command i am getting this error msg.
fail to run command '(cd easyrun; /usr/local/bin/maq map -n 2 -e 70 -u [email protected] [email protected] ref.bfa [email protected] 2> [email protected])' at ../maq-0.6.8/scripts/maq.pl line 842
can any one tell me the possible reason for this failed msg?

[kunalfab]

Same error here...

-- 0 potential soa-indels pass the filter.
-- 2 potential pe-indels pass the filter.
-- CMD: (cd easyrun; ln -s cns.final.snp cns.filter.snp)
ln: creating symbolic link `cns.filter.snp': File exists
** fail to run command '(cd easyrun; ln -s cns.final.snp cns.filter.snp)' at /usr/local/bin/maq.pl line 842.
** fail to run command '(cd maqdemo; /usr/local/bin/maq.pl easyrun -p -d easyrun ref.bfa r1.fq r2.fq)' at /usr/local/bin/maq.pl line 842.

I am new to MAQ... as well as to this forum, so kindly forgive me if i go wrong somewhere...
and kindly help in solving the above error..

[andpet]

--> ln: creating symbolic link `cns.filter.snp': File exists <--

The script tries to create a link cns.filter.snp to the file cns.final.snp. However this is not possible if the link already exists. A linux thing ...

Simply remove all files that were created by an previous maq.pl run and try again ...

Andreas

[kunalfab]

running maq on linux ubuntu 32 bit

Thanks for the reply andpet, yes what you mentioned is true and in the above case the problem was because of that only.
I had tried running after clearing the existing output files. I would like to first mention here that i am now able to successfully execute the MAQ demo. I would also like to share another piece of experience here:
I am working on a 32 bit core 2 duo, Linux machine.
Though I was able to run the maq v0.6.8 executables, directly downloaded from the sourceforge download page, i was unable to run this version compiled from source code on my machine.
Invariably I was getting stuck at the following error during execution:

---------------------------------------------------------------------------------------------------
*** buffer overflow detected ***: /home/.../maq-0.7.1/scripts/maq terminated

.
.
.

** fail to run command '(cd maqdemo; /home/.../maq-0.7.1/scripts/maq simustat easyrun/all.map > eval.simustat)' at ./maq.pl line 842.
---------------------------------------------------------------------------------------------------

Later I discovered that it was coming because of a compile time optimization parameter in the Makefile.generic:

CFLAGS= -g -Wall -O2 -m64 # comment out `-m64' for 32-bit compilation

removed the '-O2' from the above flag and changed -m64 to -m32 (as mentioned in other posts) and compiled the source code. This solved the purpose and ran the executable to completion.