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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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syntax error when execute python2 INSTALL.py core #271

Closed xpingli closed 7 years ago

xpingli commented 7 years ago

Hi metAMOS developers,

I have encountered this error during installation process

python2 INSTALL.py core

my os is ubuntu 16.04 LTS, python2 version 2.7.12

Appreciate your insight.

Thank you,

xiaoping

Finished processing dependencies for psutil==0.6.1
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  822k  100  822k    0     0   822k      0  0:00:01 --:--:--  0:00:01 5480k
pysam-0.6/
pysam-0.6/THANKS
pysam-0.6/KNOWN_BUGS
pysam-0.6/pysam.egg-info/
pysam-0.6/pysam.egg-info/PKG-INFO
pysam-0.6/pysam.egg-info/requires.txt
pysam-0.6/pysam.egg-info/dependency_links.txt
pysam-0.6/pysam.egg-info/not-zip-safe
pysam-0.6/pysam.egg-info/SOURCES.txt
pysam-0.6/pysam.egg-info/top_level.txt
pysam-0.6/samtools/
pysam-0.6/samtools/sam.c.pysam.c
pysam-0.6/samtools/kaln.c.pysam.c
pysam-0.6/samtools/cut_target.c.pysam.c
pysam-0.6/samtools/bam_tview.c.pysam.c
pysam-0.6/samtools/bam_plcmd.c.pysam.c
pysam-0.6/samtools/bam_rmdup.c.pysam.c
pysam-0.6/samtools/faidx.c.pysam.c
pysam-0.6/samtools/razf.h
pysam-0.6/samtools/bam_lpileup.c.pysam.c
pysam-0.6/samtools/bgzf.h
pysam-0.6/samtools/knetfile.h
pysam-0.6/samtools/sample.c.pysam.c
pysam-0.6/samtools/bam_rmdupse.c.pysam.c
pysam-0.6/samtools/khash.h
pysam-0.6/samtools/pysam.h
pysam-0.6/samtools/bam2bcf.h
pysam-0.6/samtools/bam_stat.c.pysam.c
pysam-0.6/samtools/kprobaln.h
pysam-0.6/samtools/bgzf.c.pysam.c
pysam-0.6/samtools/bedidx.c.pysam.c
pysam-0.6/samtools/ksort.h
pysam-0.6/samtools/bam_index.c.pysam.c
pysam-0.6/samtools/bam_cat.c.pysam.c
pysam-0.6/samtools/sam_header.c.pysam.c
pysam-0.6/samtools/bam_aux.c.pysam.c
pysam-0.6/samtools/errmod.h
pysam-0.6/samtools/win32/
pysam-0.6/samtools/win32/zconf.h
pysam-0.6/samtools/win32/zlib.h
pysam-0.6/samtools/win32/xcurses.h
pysam-0.6/samtools/bam_endian.h
pysam-0.6/samtools/klist.h
pysam-0.6/samtools/errmod.c.pysam.c
pysam-0.6/samtools/sample.h
pysam-0.6/samtools/bam2depth.c.pysam.c
pysam-0.6/samtools/bam.h
pysam-0.6/samtools/kstring.c.pysam.c
pysam-0.6/samtools/sam.h
pysam-0.6/samtools/bam.c.pysam.c
pysam-0.6/samtools/sam_view.c.pysam.c
pysam-0.6/samtools/bam_import.c.pysam.c
pysam-0.6/samtools/kseq.h
pysam-0.6/samtools/bam_color.c.pysam.c
pysam-0.6/samtools/bam_reheader.c.pysam.c
pysam-0.6/samtools/knetfile.c.pysam.c
pysam-0.6/samtools/bam_pileup.c.pysam.c
pysam-0.6/samtools/bam_sort.c.pysam.c
pysam-0.6/samtools/phase.c.pysam.c
pysam-0.6/samtools/bcftools/
pysam-0.6/samtools/bcftools/mut.c.pysam.c
pysam-0.6/samtools/bcftools/bcf2qcall.c.pysam.c
pysam-0.6/samtools/bcftools/bcfutils.c.pysam.c
pysam-0.6/samtools/bcftools/index.c.pysam.c
pysam-0.6/samtools/bcftools/bcf.h
pysam-0.6/samtools/bcftools/bcf.c.pysam.c
pysam-0.6/samtools/bcftools/prob1.h
pysam-0.6/samtools/bcftools/kmin.c.pysam.c
pysam-0.6/samtools/bcftools/fet.c.pysam.c
pysam-0.6/samtools/bcftools/kfunc.c.pysam.c
pysam-0.6/samtools/bcftools/prob1.c.pysam.c
pysam-0.6/samtools/bcftools/vcf.c.pysam.c
pysam-0.6/samtools/bcftools/em.c.pysam.c
pysam-0.6/samtools/bcftools/call1.c.pysam.c
pysam-0.6/samtools/bcftools/kmin.h
pysam-0.6/samtools/faidx.h
pysam-0.6/samtools/kaln.h
pysam-0.6/samtools/bam2bcf_indel.c.pysam.c
pysam-0.6/samtools/kprobaln.c.pysam.c
pysam-0.6/samtools/bam_mate.c.pysam.c
pysam-0.6/samtools/kstring.h
pysam-0.6/samtools/razf.c.pysam.c
pysam-0.6/samtools/bam2bcf.c.pysam.c
pysam-0.6/samtools/misc/
pysam-0.6/samtools/misc/md5.c.pysam.c
pysam-0.6/samtools/misc/md5.h
pysam-0.6/samtools/misc/seqtk.c.pysam.c
pysam-0.6/samtools/bam_md.c.pysam.c
pysam-0.6/samtools/sam_header.h
pysam-0.6/COPYING
pysam-0.6/MANIFEST.in
pysam-0.6/setup.py
pysam-0.6/INSTALL
pysam-0.6/ez_setup.py
pysam-0.6/PKG-INFO
pysam-0.6/tabix/
pysam-0.6/tabix/bgzf.h
pysam-0.6/tabix/knetfile.h
pysam-0.6/tabix/khash.h
pysam-0.6/tabix/pysam.h
pysam-0.6/tabix/index.c.pysam.c
pysam-0.6/tabix/bgzf.c.pysam.c
pysam-0.6/tabix/bedidx.c.pysam.c
pysam-0.6/tabix/tabix.h
pysam-0.6/tabix/ksort.h
pysam-0.6/tabix/bam_endian.h
pysam-0.6/tabix/kstring.c.pysam.c
pysam-0.6/tabix/kseq.h
pysam-0.6/tabix/knetfile.c.pysam.c
pysam-0.6/tabix/bgzip.c.pysam.c
pysam-0.6/tabix/kstring.h
pysam-0.6/setup.cfg
pysam-0.6/tests/
pysam-0.6/tests/ex7.sam
pysam-0.6/tests/example.gtf.gz.tbi
pysam-0.6/tests/00README.txt
pysam-0.6/tests/segfault_tests.py
pysam-0.6/tests/ex1.sam.gz
pysam-0.6/tests/example.py
pysam-0.6/tests/pysam_test.py
pysam-0.6/tests/ex9_fail.bam
pysam-0.6/tests/Makefile
pysam-0.6/tests/tabix_test.py
pysam-0.6/tests/ex9_nofail.bam
pysam-0.6/tests/ex10.sam
pysam-0.6/tests/ex1.fa
pysam-0.6/tests/ex4.sam
pysam-0.6/tests/ex5.sam
pysam-0.6/tests/example.gtf.gz
pysam-0.6/tests/ex8.sam
pysam-0.6/tests/ex6.sam
pysam-0.6/tests/ex3.sam
pysam-0.6/pysam/
pysam-0.6/pysam/version.py
pysam-0.6/pysam/ctabix.pxd
pysam-0.6/pysam/TabProxies.pyx
pysam-0.6/pysam/cvcf.pxd
pysam-0.6/pysam/csamtools.pyx
pysam-0.6/pysam/cvcf.c
pysam-0.6/pysam/namedtuple.py
pysam-0.6/pysam/__init__.py
pysam-0.6/pysam/cvcf.pyx
pysam-0.6/pysam/csamtools.pxd
pysam-0.6/pysam/Pileup.py
pysam-0.6/pysam/tabix_util.c
pysam-0.6/pysam/pysam_util.h
pysam-0.6/pysam/TabProxies.c
pysam-0.6/pysam/csamtools.c
pysam-0.6/pysam/ctabix.c
pysam-0.6/pysam/TabProxies.pxd
pysam-0.6/pysam/pysam_util.c
pysam-0.6/pysam/ctabix.pyx
mv: cannot move './Utilities/python/pysam-0.6' to './Utilities/python/pysam/pysam-0.6': Directory not empty
  File "setup.py", line 95
    print "installed latest source code from %s: %i files copied" % (srcdir, ncopied)
                                                                ^
SyntaxError: invalid syntax
  File "setup.py", line 95
    print "installed latest source code from %s: %i files copied" % (srcdir, ncopied)
                                                                ^
SyntaxError: invalid syntax
  File "setup.py", line 95
    print "installed latest source code from %s: %i files copied" % (srcdir, ncopied)
                                                                ^
SyntaxError: invalid syntax
Traceback (most recent call last):
  File "INSTALL.py", line 400, in <module>
    import numpy
  File "/home/kenfrost/Desktop/Applications/metAMOS/metAMOS-1.5rc3/Utilities/python/lib/python/numpy/__init__.py", line 131, in <module>
    from ._import_tools import PackageLoader
  File "/home/kenfrost/Desktop/Applications/metAMOS/metAMOS-1.5rc3/Utilities/python/lib/python/numpy/_import_tools.py", line 263
    print(str(mess), file=sys.stderr)
                         ^
SyntaxError: invalid syntax