As a general rule, please check the archives before posting a question: [Bfast-help] make check failed (7 of 8 tests)

Nils


On Wed, Mar 20, 2013 at 7:09 PM, Hardip Patel <hardip.patel@anu.edu.au> wrote:
Dear

I downloaded the source by following command

wget http://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz

and tried to compile the program by issuing following commands

tar -xvzf bfast-0.7.0a.tar.gz
cd bfast-0.7.0a
sh autogen.sh
./configure
make
make check


I am running Cent OS on x86 architecture.

The log after running make check is as follows:


Making check in bfast
make[1]: Entering directory `/state/partition1/apps/src/bfast-0.7.0a/bfast'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/state/partition1/apps/src/bfast-0.7.0a/bfast'
Making check in butil
make[1]: Entering directory `/state/partition1/apps/src/bfast-0.7.0a/butil'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/state/partition1/apps/src/bfast-0.7.0a/butil'
Making check in scripts
make[1]: Entering directory `/state/partition1/apps/src/bfast-0.7.0a/scripts'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/state/partition1/apps/src/bfast-0.7.0a/scripts'
Making check in tests
make[1]: Entering directory `/state/partition1/apps/src/bfast-0.7.0a/tests'
make  check-TESTS
make[2]: Entering directory `/state/partition1/apps/src/bfast-0.7.0a/tests'
./test.initialize.sh: line 3: .: test.definitions.sh: file not found
      Initializing data for tests.
mkdir: missing operand
Try `mkdir --help' for more information.
cp: omitting directory `/bin'
cp: omitting directory `/boot'
cp: omitting directory `/dev'
cp: omitting directory `/etc'
cp: omitting directory `/export'
cp: omitting directory `/home'
cp: omitting directory `/home2'
cp: omitting directory `/lib'
cp: omitting directory `/lib64'
cp: omitting directory `/lost+found'
cp: omitting directory `/media'
cp: omitting directory `/misc'
cp: omitting directory `/mnt'
cp: omitting directory `/net'
cp: omitting directory `/opt'
cp: omitting directory `/proc'
cp: omitting directory `/root'
cp: omitting directory `/sbin'
cp: omitting directory `/selinux'
cp: omitting directory `/share'
cp: omitting directory `/srv'
cp: omitting directory `/state'
cp: omitting directory `/sys'
cp: omitting directory `/tftpboot'
cp: omitting directory `/tmp'
cp: omitting directory `/usr'
cp: omitting directory `/var'
./test.fasta2brg.sh: line 3: .: test.definitions.sh: file not found
      Building a reference genome.
        Testing -A 0 CC=0
bfast fasta2brg -f .fa -A 0
./test.fasta2brg.sh: line 42: bfast: command not found
./test.index.sh: line 2: .: test.definitions.sh: file not found
      Building an index.
        Testing -A 0 CC=0
RETURN CODE=0
bfast index -f .fa -A 0 -m 111101111011101111 -w 8 -d 2 -i 1 -n -T
./test.index.sh: line 51: bfast: command not found
./test.match.sh: line 3: .: test.definitions.sh: file not found
      Finding matches.
        Testing -A 0 CC=0
bfast match -f .fa -r reads..fastq -A 0 -n -T > bfast.matches.file..bmf
./test.match.sh: line 44: bfast: command not found
./test.localalign.sh: line 3: .: test.definitions.sh: file not found
      Running local alignment.
        Testing -A 0 CC=0
bfast localalign -f .fa -m bfast.matches.file..bmf -A 0 -n -o 15 > bfast.aligned.file..baf
./test.localalign.sh: line 42: bfast: command not found
./test.postprocess.sh: line 3: .: test.definitions.sh: file not found
      Running postprocessing.
        Testing -A 0 CC=0
bfast postprocess -f .fa -i bfast.aligned.file..baf -a 3 -n > bfast.reported.file..sam
./test.postprocess.sh: line 42: bfast: command not found
./test.diff.sh: line 3: .: test.definitions.sh: file not found
      Double-checking output files.
./test.cleanup.sh: line 3: .: test.definitions.sh: file not found
      Cleaning up files.
ls: cannot open directory /lost+found: Permission denied
      Files cleaned up.
=================================================
7 of 8 tests failed
=================================================
make[2]: *** [check-TESTS] Error 1
make[2]: Leaving directory `/state/partition1/apps/src/bfast-0.7.0a/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/state/partition1/apps/src/bfast-0.7.0a/tests'
make: *** [check-recursive] Error 1


-----------------------------

Could you please let me know how to fix this issue? I am more than happy to provide any additional information that may be required to troubleshoot this problem.

Kind regards

Hardip R. Patel, PhD
Post-doctoral Research Fellow

Genome Discovery Unit and RNA Biology Lab
Genome Biology Department
The John Curtin School of Medical Research
College of Medicine, Biology and Environment
The Australian National University
Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia




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