BFAST - Help

[cutcopy11]

Hello,

I am trying to align Solid reads that map uniquely to the C. Elegans genome. I have a fastq file that has 4 lines for each read that are 50 bases in length. The reads are in color space (0-3). I have very little programming experience outside of writing simple perl scripts and am very new to next generation sequencing.

I have successfully used bowtie in the past to align reads to the human genome from Solexa data, but for some reason, I am having difficulty getting started with the latest version of BFAST. I have been reading the manual for a couple hours, which seems straightforward, but I think that there are some installation steps that I need to execute before creating the index and matching the reads.

I am working on a linux system. Could someone please tell me the commands that I need to enter to install BFAST? I entered the command, ./configure and got a response, but I think there are some additional steps that remain for the installation process.

Thanks,
cutcopy11

[nilshomer]

Originally Posted by cutcopy11

Hello,

I am trying to align Solid reads that map uniquely to the C. Elegans genome. I have a fastq file that has 4 lines for each read that are 50 bases in length. The reads are in color space (0-3). I have very little programming experience outside of writing simple perl scripts and am very new to next generation sequencing.

I have successfully used bowtie in the past to align reads to the human genome from Solexa data, but for some reason, I am having difficulty getting started with the latest version of BFAST. I have been reading the manual for a couple hours, which seems straightforward, but I think that there are some installation steps that I need to execute before creating the index and matching the reads.

I am working on a linux system. Could someone please tell me the commands that I need to enter to install BFAST? I entered the command, ./configure and got a response, but I think there are some additional steps that remain for the installation process.

Thanks,
cutcopy11

Try:
./configure
make
make install

If you need more help, post here or the bfast help mailing list: bfast-help@lists.sourceforge.net.

[cutcopy11]

Thanks for the quick response.

After performing the "./configure" and "make" commands, the "make install" command gave the following output:

~/Desktop/bfast-0.6.1c$ make install
Making install in bfast
make[1]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make[2]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/usr/bin/install -c 'bfast' '/usr/local/bin/bfast'
/usr/bin/install: cannot create regular file `/usr/local/bin/bfast': Permission denied
make[2]: *** [install-binPROGRAMS] Error 1
make[2]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make: *** [install-recursive] Error 1

Is this a problem? I see that the Bfast program is available now.

-Clayton

[nilshomer]

Originally Posted by cutcopy11

Thanks for the quick response.

After performing the "./configure" and "make" commands, the "make install" command gave the following output:

~/Desktop/bfast-0.6.1c$ make install
Making install in bfast
make[1]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make[2]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/usr/bin/install -c 'bfast' '/usr/local/bin/bfast'
/usr/bin/install: cannot create regular file `/usr/local/bin/bfast': Permission denied
make[2]: *** [install-binPROGRAMS] Error 1
make[2]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make: *** [install-recursive] Error 1

Is this a problem? I see that the Bfast program is available now.

-Clayton

Take a look at the line that says "Permission denied". Looks like you need to contact your cluster or computer administrator since you don't have sufficient privileges on the computer/cluster.

[drio]

Originally Posted by cutcopy11

Thanks for the quick response.

After performing the "./configure" and "make" commands, the "make install" command gave the following output:

~/Desktop/bfast-0.6.1c$ make install
Making install in bfast
make[1]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make[2]: Entering directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/usr/bin/install -c 'bfast' '/usr/local/bin/bfast'
/usr/bin/install: cannot create regular file `/usr/local/bin/bfast': Permission denied
make[2]: *** [install-binPROGRAMS] Error 1
make[2]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/cweaver/Desktop/bfast-0.6.1c/bfast'
make: *** [install-recursive] Error 1

Is this a problem? I see that the Bfast program is available now.

-Clayton

Come on Nils (or Nils-bot), we can do better:

1. After configure and make, your binaries/software is ready to use.
Just point your PATH env variable to /home/cweaver/Desktop/bfast-0.6.1c/bfast and you are good to go.

2. During configuring specify another location to install the software:

$ mkdir $HOME/local
$ configure --prefix=$HOME/local
$ make
$ make install

bfast will be placed in $HOME/local/bin

Good luck.

[greggrant]

I am getting the following error when I run make. Can anybody offer any advice? I am on a linux fedora 64 bit amazon cloud machine. Thanks for any help!



make all-recursive
make[1]: Entering directory `/mnt/vol3/simulations/bfast'
Making all in bfast
make[2]: Entering directory `/mnt/vol3/simulations/bfast/bfast'
gcc -Wall -g -O2 -pthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lz -lm
aflib.o: In function `AFILE_afwrite':
/mnt/vol3/simulations/bfast/bfast/aflib.c:241: undefined reference to `BZ2_bzwrite'
aflib.o: In function `AFILE_afread':
/mnt/vol3/simulations/bfast/bfast/aflib.c:185: undefined reference to `BZ2_bzRead'
/mnt/vol3/simulations/bfast/bfast/aflib.c:192: undefined reference to `BZ2_bzReadGetUnused'
/mnt/vol3/simulations/bfast/bfast/aflib.c:199: undefined reference to `BZ2_bzReadClose'
/mnt/vol3/simulations/bfast/bfast/aflib.c:207: undefined reference to `BZ2_bzReadOpen'
aflib.o: In function `AFILE_afclose':
/mnt/vol3/simulations/bfast/bfast/aflib.c:150: undefined reference to `BZ2_bzWriteClose'
aflib.o: In function `AFILE_afdopen':
/mnt/vol3/simulations/bfast/bfast/aflib.c:125: undefined reference to `BZ2_bzWriteOpen'
/mnt/vol3/simulations/bfast/bfast/aflib.c:115: undefined reference to `BZ2_bzReadOpen'
aflib.o: In function `AFILE_afopen':
/mnt/vol3/simulations/bfast/bfast/aflib.c:52: undefined reference to `BZ2_bzReadOpen'
/mnt/vol3/simulations/bfast/bfast/aflib.c:62: undefined reference to `BZ2_bzWriteOpen'
collect2: ld returned 1 exit status
make[2]: *** [bfast] Error 1
make[2]: Leaving directory `/mnt/vol3/simulations/bfast/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/vol3/simulations/bfast'
make: *** [all] Error 2

[drio]

You are missing the includes and libraries for the bzip2 library.
Try this:

$ sudo yum install bzip2 bzip2-devel bzip2-libs

and try again.

[Venkat]

Hi..
I am experiencing the same problem in Ubuntu and not able to install the package libraries also..
kindly help me out..

Thanks

[nilshomer]

Originally Posted by Venkat

Hi..
I am experiencing the same problem in Ubuntu and not able to install the package libraries also..
kindly help me out..

Thanks

Why are you unable to install the packages? Please be much more descriptive about what you tried and what is not working.

[Venkat]

I tried to compile the packages..
but its says

make all-recursive
make[1]: Entering directory `/host/bfast+bwa-0.6.4e'
Making all in bfast
make[2]: Entering directory `/host/bfast+bwa-0.6.4e/bfast'
gcc -Wall -g -O2 -pthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o bwtindex.o bwt_gen.o QSufSort.o is.o bwtmisc.o bwaseqio.o bwtio.o utils.o util.o bntseq.o bwt.o bwtgap.o stdaln.o bwtaln.o occ_results.o bwtbfast2_aux.o bwtbfast_aux.o bwtbfast2.o bwtbfast.o aflib.o Main.o -lpthread -lz -lz -lm
aflib.o: In function `AFILE_afwrite':
/host/bfast+bwa-0.6.4e/bfast/aflib.c:241: undefined reference to `BZ2_bzwrite'
aflib.o: In function `AFILE_afread':
/host/bfast+bwa-0.6.4e/bfast/aflib.c:185: undefined reference to `BZ2_bzRead'
/host/bfast+bwa-0.6.4e/bfast/aflib.c:192: undefined reference to `BZ2_bzReadGetUnused'
/host/bfast+bwa-0.6.4e/bfast/aflib.c:199: undefined reference to `BZ2_bzReadClose'
/host/bfast+bwa-0.6.4e/bfast/aflib.c:207: undefined reference to `BZ2_bzReadOpen'
aflib.o: In function `AFILE_afclose':
/host/bfast+bwa-0.6.4e/bfast/aflib.c:150: undefined reference to `BZ2_bzWriteClose'
aflib.o: In function `AFILE_afdopen':
/host/bfast+bwa-0.6.4e/bfast/aflib.c:125: undefined reference to `BZ2_bzWriteOpen'
/host/bfast+bwa-0.6.4e/bfast/aflib.c:115: undefined reference to `BZ2_bzReadOpen'
aflib.o: In function `AFILE_afopen':
/host/bfast+bwa-0.6.4e/bfast/aflib.c:52: undefined reference to `BZ2_bzReadOpen'
/host/bfast+bwa-0.6.4e/bfast/aflib.c:62: undefined reference to `BZ2_bzWriteOpen'
collect2: ld returned 1 exit status
make[2]: *** [bfast] Error 1
make[2]: Leaving directory `/host/bfast+bwa-0.6.4e/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/host/bfast+bwa-0.6.4e'
make: *** [all] Error 2

some bzip files are missing
I installed the bzip libraries and still getting same errors..

[nilshomer]

Did you install the bzip2 developers packages?

[Venkat]

I have installed the available bzip2 dev packages too..still am not getting it..

[nilshomer]

Could you run the configure script again "./configure" and post your output? Thanks for your patience.

[Venkat]

It works!!

I have configured the file and installed but did not set the path initially so..not aware where it has been installed..?
Many Thanks.

[Krosh]

Hi,
I can't install bfast in Ubuntu. Thanks for any help.

After ./configure

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
fatal: Not a git repository (or any of the parent directories): .git
checking for BZ2_bzRead in -lbz2... no
checking for an ANSI C-conforming const... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for pow in -lm... yes
checking for gzread in -lz... yes
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strpbrk... yes
checking for strstr... yes
checking for strtok_r... yes
checking for int8_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking size of short int... 2
checking size of int... 4
checking size of long int... 8
checking for ANSI C header files... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking bzlib.h usability... no
checking bzlib.h presence... no
checking for bzlib.h... no
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bfast/Makefile
config.status: creating butil/Makefile
config.status: creating scripts/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

After make

make all-recursive
make[1]: Вход в каталог `/media/share/bfast-0.6.4e'
Making all in bfast
make[2]: Вход в каталог `/media/share/bfast-0.6.4e/bfast'
gcc -DHAVE_CONFIG_H -I. -I.. -Wall -g -O2 -pthread -MT MatchesReadInputFiles.o -MD -MP -MF .deps/MatchesReadInputFiles.Tpo -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c
In file included from MatchesReadInputFiles.c:10:
aflib.h:6: fatal error: bzlib.h: Нет такого файла или каталога
compilation terminated.
make[2]: *** [MatchesReadInputFiles.o] Ошибка 1
make[2]: Выход из каталога `/media/share/bfast-0.6.4e/bfast'
make[1]: *** [all-recursive] Ошибка 1
make[1]: Выход из каталога `/media/share/bfast-0.6.4e'
make: *** [all] Ошибка 2

[nilshomer]

Originally Posted by Krosh

Hi,
I can't install bfast in Ubuntu. Thanks for any help.

Same answer, install the necessary packages listed above. I am adding this to the new BFAST FAQ: https://sourceforge.net/apps/mediawi....php?title=FAQ

[Krosh]

Thank you!

[hkg]

Hi,

I am also having some problems building bfast (0.7.0a) on mac osx 10.8.5 with xcode version 3.2.6.

I am able to run the autogen.sh and ./configure successfully, but I get the following error during the make:

Undefined symbols for architecture x86_64:
"_AlignNTSpaceFillInCell", referenced from:
_AlignNTSpaceGappedBounded in AlignNTSpace.o
_AlignNTSpaceGappedConstrained in AlignNTSpace.o
"_ScoringMatrixGetColorScore", referenced from:
_AlignExact in Align.o
_AlignColorSpaceUngappedGetBest in AlignColorSpace.o
_AlignColorSpaceFillInCell in AlignColorSpace.o
_AlignColorSpaceGappedConstrained in AlignColorSpace.o
"_ScoringMatrixGetNTScore", referenced from:
_AlignExact in Align.o
_AlignNTSpaceUngapped in AlignNTSpace.o
_AlignNTSpaceGappedConstrained in AlignNTSpace.o
_AlignColorSpaceUngappedGetBest in AlignColorSpace.o
_AlignColorSpaceFillInCell in AlignColorSpace.o
_AlignColorSpaceGappedConstrained in AlignColorSpace.o
"_ToUpper", referenced from:
_AlignedReadConvertPrintAlignedEntryToCIGAR in AlignedReadConvert.o
_RGBinaryRead in RGBinary.o
_RGMatchCheck in RGMatch.o
_AlignExact in Align.o
(maybe you meant: _ToUpperRead)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [bfast] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Searching online leads me to believe that it is a problem in the linking stage, but I don't know how to fix it myself. If anyone has any tips for me, or if I need to post more information, then please let me know.