TopHat installation fails

[affi]

Hi ,

Tried installing tophat-2.0.10 . But while doing make it flags following error -

/usr/local/samtools-0.1.19/bgzf.c:409: undefined reference to `__sync_fetch_and_add_4'
collect2: ld returned 1 exit status
make[2]: *** [prep_reads] Error 1
make[2]: Leaving directory `/home/aftab/Desktop/NGS/tophat-2.0.10/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/aftab/Desktop/NGS/tophat-2.0.10'
make: *** [all] Error 2

Please help .

[GenoMax]

What OS are you using? Is it 64-bit/32-bit? Are you using the latest gcc compiler?

[affi]

What OS are you using? Is it 64-bit/32-bit? Are you using the latest gcc compiler?

Its 32bit centos 5.6 . and GCC version 4.1.2

[GenoMax]

You are using a very old version of GCC (current release is 4.8.2). Is there a possibility that you can upgrade?

On a different note: If you are going to work with small genomes 32-bit OS may be ok but for large genomes (e.g. human/mouse) that would become a limitation.

Is this a virtual machine or a real server?

[affi]

You are using a very old version of GCC (current release is 4.8.2). Is there a possibility that you can upgrade?

On a different note: If you are going to work with small genomes 32-bit OS may be ok but for large genomes (e.g. human/mouse) that would become a limitation.

Is this a virtual machine or a real server?

Thanks . Will upgrade and try once again . Yeah mostly going to work on human genome . Most software flags out of memory on 32 bit . Also it normal i5 machine .

[affi]

Thanks . Will upgrade and try once again . Yeah mostly going to work on human genome . Most software flags out of memory on 32 bit . Also it normal i5 machine .

Updated the GCC version . The previous error was resolved however make again failed with the following error -

/home/aftab/Desktop/NGS/software/bin/lib/libbam.a(bgzf.o): In function `worker_aux':
/usr/local/samtools-0.1.19/bgzf.c:409: undefined reference to `__sync_fetch_and_add_4'
/home/aftab/Desktop/NGS/software/bin/lib/libbam.a(bgzf.o): In function `mt_destroy':
/usr/local/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
/home/aftab/Desktop/NGS/software/bin/lib/libbam.a(bgzf.o): In function `bgzf_mt':
/usr/local/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
make[2]: *** [prep_reads] Error 1
make[2]: Leaving directory `/home/aftab/Desktop/NGS/tophat-2.0.10/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/aftab/Desktop/NGS/tophat-2.0.10'
make: *** [all] Error 2

Am i missing something ? Please help .

[GenoMax]

Are you still using 32-bit CentOS?

[affi]

Are you still using 32-bit CentOS?

Yes am still using 32-bit centos . Is that the reason for the failed compilation ? . Am installing 64bit today . Will check again on that .

Thanks again .

[GenoMax]

Possibly. See the -march flag in the answer here: http://stackoverflow.com/questions/7...etch-and-add-4 If you want to try that.

That said for human samples I would advise moving to 64-bit OS. You will be glad you did. Hope you have > 4GB RAM installed.

[affi]

Possibly. See the -march flag in the answer here: http://stackoverflow.com/questions/7...etch-and-add-4 If you want to try that.

That said for human samples I would advise moving to 64-bit OS. You will be glad you did. Hope you have > 4GB RAM installed.

Yeah its's 8 core with 8GB RAM . Hope that helps . Will try the installation on Monday on 64bit .

Thanks again .