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Old 08-11-2008, 09:59 AM   #1
kwebb
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Default SOAP on Mac Pro

Hi

I am trying to run SOAP on a Mac Pro 2 × quad-core 2.8 GHz machine. When I try to run soap I get the following error:

>soap -a reads.fastq -d ref.txt -o soap.out
Start at: Mon Aug 11 13:51:22 2008

Load in 1 db seqs, total size 117080 bp. 0 secs passed
total_kmers: 1048576
Create seed table. 0 secs passed
Single read alignment:
Query: reads.fastq Reference: ref.txt Output: soap.out
Segmentation fault

I have emailed with the SOAP authors and was told that SOAP cannot be run on my machine because it's only 32 bit and that I should try it on a 64 bit machine. But I'm fairly certain the new Mac Pros are 64 bit - and I don't have access to another machine. I have been playing around with the -arch in the makefile but haven't found an option that solves my problem.

Has anyone experienced a similar problem and found a way around it?
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Old 08-11-2008, 10:47 AM   #2
Chipper
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I think I got "segmentation fault" once when the input file (sequences) was not formatted correctly, perhaps it does not recognize fastq format? Try to convert it to fasta instead.
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Old 08-11-2008, 10:59 AM   #3
kwebb
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Thanks - I tried it but still get the same error.
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Old 08-11-2008, 06:26 PM   #4
zee
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There is an alternative to SOAP available on the Mac OS , you can get it at http://www.novocraft.com/downloads/download.html

I've run it successfully on my Macbook Pro.
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Old 08-11-2008, 11:52 PM   #5
sigusn
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Im having exact the same problem with SOAP on my MacBook Pro. But the Novoalign software works OK.
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Old 08-12-2008, 01:18 AM   #6
tjahns
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Default Building 64bit Software on Mac OS X

Unless you are actually running Linux on your Mac Pro, you will need to add -m64 to the CFLAGS, CXXFLAGS (if C++ source) and LDFLAGS for the standard toolchain (i.e. the one you install from the XCode package) to produce 64 bit executables and objects.

Also of importance: only in 10.5 aka Leopard are all libraries in 64 bit format, in 10.4 everything but the system libraries (libc, libstdc++) is 32bit only i.e. libbz2.

Greetings,
Thomas Jahns

Last edited by tjahns; 08-12-2008 at 03:28 AM.
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Old 08-12-2008, 05:45 AM   #7
kwebb
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Thanks tjahns. I think your recommendation is what I need. I am working in Leopard - 10.5.4 and I have XCode installed. How do I add the -m64? Could you please give detailed instructions?

Also - I have installed Novocraft and also have it running on my machine.

Thanks all!
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Old 08-12-2008, 05:58 AM   #8
lh3
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You should edit makefile and modify the FLAGS line to:

FLAGS= -static -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3 -m64

However, I do not think this is caused by -m64. SOAP is expected to work with 32-bit machines. I guess SOAP's random crashes are due to hidden bugs. I would recommend to use novocraft. It is a lot better in my own opinion.
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Old 08-12-2008, 06:08 AM   #9
kwebb
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Thanks. I had tried that previously and still got the same error. Although I had to change the -static to -dynamiclib to get it to make.
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Old 08-12-2008, 06:21 AM   #10
tjahns
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The recommendation by lh3 is correct. But since the authors of SOAP do not distinguish CC from CXX and the diverse types of *FLAGS from one another, they probably lack the necessary experience to write POSIX conformant software. That means you would probably have to compile the program with -g and load it in gdb to analyze the problem. But I wouldn't recommend that unless you are relatively well versed in programming and debugging.
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