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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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after changing python to python2 in runProgressiveCactus.sh, still print error #98

Closed cistarsa closed 6 years ago

cistarsa commented 6 years ago

Success with help output when I changed python to python2:

/bin/runProgressiveCactus.sh 
Usage: runProgressiveCactus.sh [options] <seqFile> <workDir> <outputHalFile>

Required Arguments:
  <seqFile>     File containing newick tree and seqeunce paths paths.
            (see documetation or examples for format).
  <workDir>     Working directory (which can grow exteremely large)
  <outputHalFile>   Path of output alignment in .hal format.

but when I did a test run, I got another print error: 

$ ./bin/runProgressiveCactus.sh Lrubi_ldec.txt WD Ldec_Lrubi 

Beginning Alignment
Traceback (most recent call last):
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/bin/cactus_createMultiCactusProject.py", line 16, in <module>
    from cactus.progressive.multiCactusProject import MultiCactusProject
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 23, in <module>
    from cactus.progressive.multiCactusTree import MultiCactusTree
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusTree.py", line 22, in <module>
    from sonLib.nxnewick import NXNewick
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/sonLib/nxnewick.py", line 190
    print "PRE"
              ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(int "PRE")?
Error: Command: cactus_createMultiCactusProject.py "/home/molecularecology/Desktop/BWA/progressiveCactus/WD/expTemplate.xml" "WD/progressiveAlignment" --fixNames=0 exited with non-zero status 1

head Lrubi_ldec.txt 

## for seqfile:
Ldec_redundans_on_alpaths_contigs_genome /home/molecularecology/Desktop/BWA/Reads_Maps/Ldec_redundans_on_alpaths_contigs_genome.fa
Scaffolds_pass1.fa /home/molecularecology/Desktop/BWA/BESST_noscore/BESST_output/pass1/Scaffolds_pass1.fa
diekhans commented 6 years ago

looks like it's still running python3

Perhaps the easiest fix is to put program named python in your PATH that is python2. This could probably be a symlink from python2.

kingcohn1 notifications@github.com writes:

Success with help output when I changed python to python2:

/bin/runProgressiveCactus.sh Usage: runProgressiveCactus.sh [options]

Required Arguments:

File containing newick tree and seqeunce paths paths. (see documetation or examples for format). Working directory (which can grow exteremely large) Path of output alignment in .hal format. but when I did a test run, I got another print error: $ ./bin/runProgressiveCactus.sh Lrubi_ldec.txt WD Ldec_Lrubi Beginning Alignment Traceback (most recent call last): File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/bin/cactus_createMultiCactusProject.py", line 16, in from cactus.progressive.multiCactusProject import MultiCactusProject File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 23, in from cactus.progressive.multiCactusTree import MultiCactusTree File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusTree.py", line 22, in from sonLib.nxnewick import NXNewick File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/sonLib/nxnewick.py", line 190 print "PRE" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(int "PRE")? Error: Command: cactus_createMultiCactusProject.py "/home/molecularecology/Desktop/BWA/progressiveCactus/WD/expTemplate.xml" "WD/progressiveAlignment" --fixNames=0 exited with non-zero status 1 head Lrubi_ldec.txt ## for seqfile: Ldec_redundans_on_alpaths_contigs_genome /home/molecularecology/Desktop/BWA/Reads_Maps/Ldec_redundans_on_alpaths_contigs_genome.fa Scaffolds_pass1.fa /home/molecularecology/Desktop/BWA/BESST_noscore/BESST_output/pass1/Scaffolds_pass1.fa — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.*
cistarsa commented 6 years ago

Ok I’ll try that! Thanks, Mark.

On Thu, Jan 4, 2018 at 6:12 PM Mark Diekhans notifications@github.com wrote:

looks like it's still running python3

Perhaps the easiest fix is to put program named python in your PATH that is python2. This could probably be a symlink from python2.

kingcohn1 notifications@github.com writes:

Success with help output when I changed python to python2:

/bin/runProgressiveCactus.sh Usage: runProgressiveCactus.sh [options]

Required Arguments: File containing newick tree and seqeunce paths paths. (see documetation or examples for format). Working directory (which can grow exteremely large) Path of output alignment in .hal format. but when I did a test run, I got another print error: $ ./bin/runProgressiveCactus.sh Lrubi_ldec.txt WD Ldec_Lrubi Beginning Alignment Traceback (most recent call last): File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/bin/cactus_createMultiCactusProject.py", line 16, in from cactus.progressive.multiCactusProject import MultiCactusProject File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 23, in from cactus.progressive.multiCactusTree import MultiCactusTree File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusTree.py", line 22, in from sonLib.nxnewick import NXNewick File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/sonLib/nxnewick.py", line 190 print "PRE" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(int "PRE")? Error: Command: cactus_createMultiCactusProject.py "/home/molecularecology/Desktop/BWA/progressiveCactus/WD/expTemplate.xml" "WD/progressiveAlignment" --fixNames=0 exited with non-zero status 1 head Lrubi_ldec.txt ## for seqfile: Ldec_redundans_on_alpaths_contigs_genome /home/molecularecology/Desktop/BWA/Reads_Maps/Ldec_redundans_on_alpaths_contigs_genome.fa Scaffolds_pass1.fa /home/molecularecology/Desktop/BWA/BESST_noscore/BESST_output/pass1/Scaffolds_pass1.fa — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.*

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/98#issuecomment-355436685, or mute the thread https://github.com/notifications/unsubscribe-auth/AT5bu1gXtlnyVtfwLUMmsnk847xJWpuuks5tHWjigaJpZM4RT3rP .

cistarsa commented 6 years ago

still a bit amiss here. I tried changing the alias using


$ sudo update-alternatives --install /usr/bin/python python /usr/bin/python2.7 1
$ sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.5 2
$ update-alternatives --list python
/usr/bin/python2.7
/usr/bin/python3.5
# check version
$ python -V
Python 2.7.12
# and
alias python=python2
#and 
alias python=python2.7
# the version still shows 2.7.12
diekhans commented 6 years ago

2.7.* is great. The problem with the print statement is with 3.0.

Alias is only for your local shell it will not impact anything It seems your default `python' is now 2.7.12.

Give cactus a try

kingcohn1 notifications@github.com writes:

still a bit amiss here. I tried changing the alias using

$ sudo update-alternatives --install /usr/bin/python python /usr/bin/python2.7 1 $ sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.5 2 $ update-alternatives --list python /usr/bin/python2.7 /usr/bin/python3.5

check version

$ python -V Python 2.7.12

and

alias python=python2

and

alias python=python2.7

the version still shows 2.7.12

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.*

cistarsa commented 6 years ago

OK so as the default seems to be 2.7.12, why am I still getting the same print error? 

$ python -V
Python 2.7.12

Beginning Alignment
Traceback (most recent call last):
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/bin/cactus_createMultiCactusProject.py", line 16, in <module>
    from cactus.progressive.multiCactusProject import MultiCactusProject
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 23, in <module>
    from cactus.progressive.multiCactusTree import MultiCactusTree
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/cactus/progressive/multiCactusTree.py", line 22, in <module>
    from sonLib.nxnewick import NXNewick
  File "/home/molecularecology/Desktop/BWA/progressiveCactus/submodules/sonLib/nxnewick.py", line 190
    print "PRE"
              ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(int "PRE")?
Error: Command: cactus_createMultiCactusProject.py "/home/molecularecology/Desktop/BWA/progressiveCactus/WD/expTemplate.xml" "WD/progressiveAlignment" --fixNames=0 exited with non-zero status 1

Temporary data was left in: WD
More information can be found in WD/cactus.log

thank you

cistarsa commented 6 years ago

I rebuilt on a system that only has python 2.6.6 and it worked!