invalid syntax

[anubhabkhan]

Hi,

I just started using progressive Cactus. I get the following error: Traceback (most recent call last): File "path/progressiveCactus/bin/./../src/progressiveCactus.py", line 37, in from sonLib.bioio import logger File "path/progressiveCactus/submodules/sonLib/bioio.py", line 719 valid_chars = {x for x in string.ascii_letters + "-"} ^ SyntaxError: invalid syntax

My input was: path/progressiveCactus/bin/./runProgressiveCactus.sh --maxThreads 100 path/reference.fasta path/wrdir path/wrdir

I am unable to understand what went wrong. can someone help?

thanks

[glennhickey]

Are you using Python 2.7?

On Sun, Dec 4, 2016 at 4:18 AM, anubhabkhan notifications@github.com wrote:

Hi,

I just started using progressive Cactus. I get the following error: Traceback (most recent call last): File "path/progressiveCactus/bin/./../src/progressiveCactus.py", line 37, in from sonLib.bioio import logger File "path/progressiveCactus/submodules/sonLib/bioio.py", line 719 valid_chars = {x for x in string.ascii_letters + "-"} ^ SyntaxError: invalid syntax

My input was: path/progressiveCactus/bin/./runProgressiveCactus.sh --maxThreads 100 path/reference.fasta path/wrdir path/wrdir

I am unable to understand what went wrong. can someone help?

thanks

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[anubhabkhan]

my python 2.7 was not getting called by default. now I changed the following line in the .sh file: {envFile} && eval python2.7 ${binDir}/../src/progressiveCactus.py "$options"

but now I get the following error: Traceback (most recent call last): File "path/progressiveCactus/bin/./../src/progressiveCactus.py", line 48, in from cactus.progressive.multiCactusProject import MultiCactusProject File "path/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 23, in from cactus.progressive.multiCactusTree import MultiCactusTree File "path/progressiveCactus/submodules/cactus/progressive/multiCactusTree.py", line 21, in from sonLib.nxtree import NXTree File "path/progressiveCactus/submodules/sonLib/nxtree.py", line 18, in import networkx as NX ImportError: No module named networkx

[anubhabkhan]

Hi, Do you think the problem is because of the scheduler I use? The cluster I use is a torque scheduler.

thanks

[jq2252]

I have the same problem. I can run it in my mac with python 2.7. But When I run it in redhat 6.9, with python 2.7 or python 3.6, there is exception as following: Traceback (most recent call last): File "bin/../src/progressiveCactus.py", line 37, in from sonLib.bioio import logger File "/progressiveCactus/submodules/sonLib/bioio.py", line 719 valid_chars = {x for x in string.ascii_letters + "-"} with python --version Python 2.7.13 :: Anaconda 4.4.0 (64-bit) or python --version Python 3.6.1 :: Anaconda 4.4.0 (64-bit)