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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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AttributeError: 'module' object has no attribute 'cached_phymem' #241

Closed ghost closed 8 years ago

ghost commented 8 years ago

Hi

I am trying to install metAMOS but ran into this error:

~/software/metAMOS-1.5rc3> python INSTALL.py core <> Selected to install workflowName: CORE. Will automatically install: Pysam Setuptools Fastqc Matplotlib Metavelvet Lap Kronatools Cython Sra Velvet Velvet-Sc Kraken Psutil Uniprot Amos Numpy Traceback (most recent call last): File "INSTALL.py", line 511, in mem = utils.getAvailableMemory(settings) File "/nfs/homeserver/phylosopher/u/ksoh/software/metAMOS-1.5rc3/src/utils.py", line 1283, in getAvailableMemory cacheusage = psutil.cached_phymem() AttributeError: 'module' object has no attribute 'cached_phymem'

treangen commented 8 years ago

hi kengcher,

Are you running on OSX or Linux?

mukul1992 commented 8 years ago

Hi,

I am also hitting the same error, I guess because 'cached_phymem' may be deprecated. This is on Linux CentOS 6.7. Is there a workaround?

mukul1992 commented 8 years ago

Temporarily uninstalling psutil works as then metAMOS install script downloads and use its own compatible version.

skoren commented 8 years ago

metAMOS has only been tested with a specific psutil version, the next release should update to the most recent version. Closing as workaround is to let metAMOS install compatible version.

mhibberd commented 7 years ago

Hey All, I realize this issue has been closed, but I'm still experiencing troubles with the psutil version. The stated version of psutil for metAMOS is 0.6.1, although the above messages suggest there would have been an update to accommodate newer versions. I'm on psutil 3.4.2 and am seeing the "cached_phymem" error at runtime with runPipeline. Any suggestions? I'm on a cluster environment so changing the psutil version backward is slightly less trivial than on a local system. Thanks!

dvera commented 7 years ago

You could try installing your own copy of python and changing your PATH to use your version.

hiraksarkar commented 6 years ago

Just to comment that this issue is not resolved and the version of psutil currently in use should be mentioned in the required versions in README page.

skoren commented 6 years ago

The version requirements are documented: http://metamos.readthedocs.io/en/v1.5rc3/content/installation.html