[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.

[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]

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..

[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?

[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

[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]

Maq problems

I have just noticed this error when compiling maq-0.6.8 with 'make'

ld64 warning: in /usr/lib/libz.dylib, file is not of required architecture

I am running it on a PowerPC G4 Mac but also get the same error on a G5

even though the Maq webpage says that - "Compiling as a 32bit executable should work but the speed will be affected"

Do I just need to somehow get different libraries or should I just give up now !!!

exasperated alig

[alig]

Maq problems

Hi Eco,

Yes it's a Mac OS X 10.4.11 & so has Xcode 2.4.1 installed on it.

but the autoconf is only version 2.59 & gm4 is version 1.4.2

So I was trying to install more recent versions. But it's still looking at the built-ins & not the newer more recently installed versions

alig

[ECO]

Looks like that's a Mac...have you installed the developers tools ("Xcode" if i remember correctly) ??

[alig]

Hi Andreas,

When I type 'make' I get this error message

/Documents/Alison/Maq/maq-0.6.8 jozefgecz$ make
cd . && /bin/sh /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/missing --run autoheader
aclocal.m4:17: error: this file was generated for autoconf 2.61.
You have another version of autoconf. If you want to use that,
you should regenerate the build system entirely.
aclocal.m4:17: the top level
autom4te: /usr/bin/gm4 failed with exit status: 63
autoheader: /usr/bin/autom4te failed with exit status: 63
WARNING: `autoheader' is probably too old. You should only need it if
you modified `acconfig.h' or `configure.ac'. You might want
to install the `Autoconf' and `GNU m4' packages. Grab them
from any GNU archive site.

......and at the very end - ld64-62.1 failed: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [maq] Error 1
make: *** [all] Error 2


I have downloaded & compiled autoconf 2.61 & GNU M4 1.4.9 but it still seems to be finding the built-ins (You have another version of autoconf) & not the newer version just installed.

alig

[valeu]

Hrm. I had nothing but problems with 0.7.0 and 0.7.1, so went back to 0.6.8.

Did you compile maq?

Oh thank you so much! I tried everything to make maq 0.7.1 work! I managed to compile it but then I got "Segmentation error" trying to run it..
And with 0.6.8 it's fine!

Valentina

[andpet]

getting maq started

Hi,

the file maq.1 is definitly the man page, so it makes no sense to rename it to get the executable. The missing executable seems to be the problem

Maybe it is the best if you recompile your maq version (make clean first then ./configure; make; make install) and post any errors that occurred ?

Andreas

[alig]

Maq problems

I did compile maq, but I can never find a maq executable

The maq.pl & maq_eval.pl scripts come in maqview I think, & I have them

but there is only maq.1 not maq so I always get the ouput

maq.pl easyrun -d outdir ref.fasta reads.fastq
[gwhich] fail to find executable maq anywhere. at /usr/bin/maq.pl line 883.
** Cannot find 'maq' executable. at /usr/bin/maq.pl line 77.

alig

[alig]

maq problems

I renamed the script...maq.1 as it was looking for maq in the same directory as maq.pl & maq_eval.pl & couldn't find maq as there wasn't a file of that name I assumed.

That is probably my problem then if it is actually the man pages. I might try an earlier version then - 0.6.8

thanks a lot for all your help so far everyone

alig

[xuer]

maybe you have fixed the froblem.if not,
look the command below, are you using calib-30.dat or calib-36.dat?

maybe it is the reason. if you can see the message soon.

-- CMD: /usr/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta
calib-30.dat > maqdemo/true.snp