pysam local install erron on Mac

Yung-Chih Lai

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Mar 22, 2017, 11:37:27 PM3/22/17

to Pysam User group

Hi,

I have a problem to local install pysam on my MacBook Pro notebook. Could you help me? Please see the detail below.

1. My htseq-count cannot find the pysam, it is the same problem I google: https://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/dyer/software/htseq/

gary > pwd

/Users/gary/Downloads/htseq

gary > ll

total 2075280

-rwxr-xr-x@ 1 gary staff 966M Mar 14 08:41 Chuong569.bam

-rw-r--r--@ 1 gary staff 47M Mar 3 10:40 galGal4UCSCensGene81_TableBrowser.gtf

gary > htseq-count -f bam -s no -a 10 -t exon -i gene_id -m union Chuong569.bam galGal4UCSCensGene81_TableBrowser.gtf > L_FE9D_R569.txt

100000 GFF lines processed.

200000 GFF lines processed.

300000 GFF lines processed.

386159 GFF lines processed.

Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/)Error occured when reading beginning of SAM/BAM file.

No module named pysam

[Exception type: ImportError, raised in __init__.py:937]

gary >

2. The below shows directories I can find pysam on my notebook, but no one can be found by htseq-count

gary > cd /Users/gary/anaconda/pkgs/pysam-0.8.4-py27_0/lib/python2.7/site-packages/pysam/

gary > ls

Pileup.py cbcf.pxd csamtools.so cvcf.so samfile_util.h

Pileup.pyc cbcf.so ctabix.pxd htslib_util.h tabix_util.h

__init__.py cfaidx.pxd ctabix.so include/ version.py

__init__.pyc cfaidx.so ctabixproxies.pxd libchtslib.so version.pyc

calignedsegment.pxd chtslib.pxd ctabixproxies.so namedtuple.py

calignedsegment.so csamfile.pxd cutils.pxd namedtuple.pyc

calignmentfile.pxd csamfile.so cutils.so pysam_stream.h

calignmentfile.so csamtools.pxd cvcf.pxd pysam_util.h

gary > cd /Users/gary/anaconda/pkgs/pysam-0.8.4-py27_0/lib/python2.7/site-packages/pysam-0.8.4-py2.7-macosx-10.5-x86_64.egg-info/

gary > ls

PKG-INFO dependency_links.txt not-zip-safe

SOURCES.txt native_libs.txt top_level.txt

gary > cd /Users/gary/anaconda/pkgs/pysam-0.8.4-py27_0/

gary > ls

info/ lib/

gary > cd /Users/gary/anaconda/lib/python2.7/site-packages/pysam-0.8.4-py2.7-macosx-10.5-x86_64.egg-info/

gary > ls

PKG-INFO dependency_links.txt not-zip-safe

SOURCES.txt native_libs.txt top_level.txt

gary > cd /Users/gary/anaconda/lib/python2.7/site-packages/pysam-0.8.4.dist-info/

gary > ls

DESCRIPTION.rst RECORD metadata.json

METADATA WHEEL top_level.txt

3. I followed the instruction below to install pysam, but it doesn’t work, and show error messages below

Instruction (https://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/dyer/software/htseq/)

Intalling pysam using pip does not seem to work as pip does not support a local install and only a root install. Instead, download pysam from https://pypi.python.org/pypi/pysam, unpack and then then 'python setup.py build' and 'python setup.py install --prefix /cluster/nigeldyer/local' as before to do a local installation of pysam

Installation of pysam

gary > pwd

/Users/gary

gary > cd Applications/

gary > ls

Aspera Connect.app/ bedGraphToBigWig

Aspera Crypt.app/ bedSort

CEAS-Package-1.0.2/ bedToBigBed

Chrome Apps.localized/ bigWigToBedGraph

Flux.app/ bowtie2-2.3.0/

HTSeq-0.6.1/ fetchChromSizes

HiC-Pro-master/ genePredToGtf

HiC-Pro_2.8.1_devel/ hgWiggle

ROSE/ homer/

Trimmomatic-0.36/ mafSplit

Utilities/ pysam-0.10.0/

Wineskin/ qualimap-build-24-09-15/

Wineskin Winery.app/ rar/

axtToMaf sratoolkit.2.8.1-2-mac64/

bamUtil/ weblogo/

bedClip wigToBigWig

gary > cd pysam-0.10.0/

gary > ll

total 112

-rw-r--r--@ 1 gary staff 1.1K Nov 1 03:46 COPYING

-rw-r--r--@ 1 gary staff 1.4K Nov 1 03:46 INSTALL

-rw-r--r--@ 1 gary staff 1.8K Nov 1 04:00 MANIFEST.in

-rw-r--r--@ 1 gary staff 1.1K Jan 23 04:58 PKG-INFO

-rw-r--r--@ 1 gary staff 1.5K Nov 1 03:46 README.rst

drwxr-xr-x@ 50 gary staff 1.7K Jan 23 04:58 bcftools/

-rw-r--r--@ 1 gary staff 3.1K Jan 6 05:12 cy_build.py

drwxr-xr-x@ 13 gary staff 442B Jan 23 04:58 doc/

drwxr-xr-x@ 34 gary staff 1.1K Jan 23 04:58 htslib/

drwxr-xr-x@ 52 gary staff 1.7K Jan 23 04:58 pysam/

drwxr-xr-x@ 7 gary staff 238B Jan 23 04:58 pysam.egg-info/

-rw-r--r--@ 1 gary staff 134B Nov 1 03:46 pysam.py

-rw-r--r--@ 1 gary staff 15B Nov 1 03:46 requirements.txt

drwxr-xr-x@ 65 gary staff 2.2K Jan 23 04:58 samtools/

-rw-r--r--@ 1 gary staff 59B Jan 23 04:58 setup.cfg

-rw-r--r--@ 1 gary staff 17K Jan 8 08:32 setup.py

drwxr-xr-x@ 17 gary staff 578B Jan 23 04:58 tests/

gary > python setup.py build

# pysam: cython is available - using cythonize if necessary

# pysam: htslib mode is shared

# pysam: HTSLIB_CONFIGURE_OPTIONS=None

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for ranlib... ranlib

checking for special C compiler options needed for large files... no

checking for _FILE_OFFSET_BITS value needed for large files... no

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for stdlib.h... (cached) yes

checking for unistd.h... (cached) yes

checking for sys/param.h... yes

checking for getpagesize... yes

checking for working mmap... yes

checking for gmtime_r... yes

checking for zlib.h... yes

checking for inflate in -lz... yes

checking for curl_easy_pause in -lcurl... yes

checking for CCHmac... yes

configure: creating ./config.status

config.status: creating config.mk

config.status: creating config.h

# pysam: htslib configure options: --enable-libcurl

# pysam: htslib_config LIBS=-lcurl

# pysam: htslib_config PLATFORM=Darwin

# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o hfile_libcurl.o

# pysam: htslib_config LDFLAGS=

# pysam: config_option: ENABLE_PLUGINS=0

# pysam: config_option: HAVE_COMMONCRYPTO=1

# pysam: config_option: HAVE_GMTIME_R=1

# pysam: config_option: HAVE_HMAC=0

# pysam: config_option: HAVE_IRODS=0

# pysam: config_option: HAVE_LIBCURL=1

# pysam: config_option: HAVE_MMAP=1

running build

running build_py

creating build

creating build/lib.macosx-10.5-x86_64-2.7

creating build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/bcftools.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/config.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/namedtuple.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/Pileup.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/samtools.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/utils.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/version.py -> build/lib.macosx-10.5-x86_64-2.7/pysam

creating build/lib.macosx-10.5-x86_64-2.7/pysam/include

copying pysam/include/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pysam/include

package init file 'samtools/__init__.py' not found (or not a regular file)

package init file 'bcftools/__init__.py' not found (or not a regular file)

package init file 'samtools/win32/__init__.py' not found (or not a regular file)

package init file 'htslib/__init__.py' not found (or not a regular file)

package init file 'htslib/htslib/__init__.py' not found (or not a regular file)

copying pysam/libcalignedsegment.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libcalignmentfile.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libcbcf.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libcfaidx.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libchtslib.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libcsamfile.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libctabix.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libctabixproxies.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libcutils.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/libcvcf.pxd -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/htslib_util.h -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/pysam_stream.h -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/pysam_util.h -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/samfile_util.h -> build/lib.macosx-10.5-x86_64-2.7/pysam

copying pysam/tabix_util.h -> build/lib.macosx-10.5-x86_64-2.7/pysam

creating build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/bam.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/bam2bcf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/bam_endian.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/bam_lpileup.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/bam_plbuf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/bam_tview.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/config.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/errmod.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/kprobaln.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/pysam.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/sam.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/sam_header.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/sam_opts.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/sample.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/samtools.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/stats_isize.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

copying samtools/version.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools

creating build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/bcftools.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/call.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/convert.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/filter.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/gvcf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/HMM.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/khash_str2str.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/kmin.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/ploidy.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/prob1.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/pysam.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/rbuf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/tsv2vcf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/vcmp.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

copying bcftools/version.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/bcftools

creating build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools/win32

copying samtools/win32/xcurses.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools/win32

copying samtools/win32/zconf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools/win32

copying samtools/win32/zlib.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/samtools/win32

creating build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib

copying htslib/config.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib

copying htslib/hfile_internal.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib

copying htslib/hts_internal.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib

copying htslib/version.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib

creating build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/bgzf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/cram.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/faidx.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/hfile.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/hts.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/hts_defs.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/kbitset.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/kfunc.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/khash.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/khash_str2int.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/klist.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/knetfile.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/kseq.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/ksort.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/kstring.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/regidx.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/sam.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/tbx.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/vcf.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.5-x86_64-2.7/pysam/include/htslib/htslib

running build_ext

cythoning pysam/libchtslib.pyx to pysam/libchtslib.c

building 'pysam.libchtslib' extension

creating build/temp.macosx-10.5-x86_64-2.7

creating build/temp.macosx-10.5-x86_64-2.7/pysam

creating build/temp.macosx-10.5-x86_64-2.7/htslib

creating build/temp.macosx-10.5-x86_64-2.7/htslib/cram

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libchtslib.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/htslib_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/kfunc.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/knetfile.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/kstring.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/bgzf.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/faidx.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/hfile.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/hfile_net.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/hts.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/md5.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/regidx.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/sam.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/tbx.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/vcf.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/vcfutils.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_external.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/files.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/rANS_static.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/vlen.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/vlen.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/cram/zfio.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/zfio.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c htslib/hfile_libcurl.c -o build/temp.macosx-10.5-x86_64-2.7/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libchtslib.o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o build/temp.macosx-10.5-x86_64-2.7/htslib/kfunc.o build/temp.macosx-10.5-x86_64-2.7/htslib/knetfile.o build/temp.macosx-10.5-x86_64-2.7/htslib/kstring.o build/temp.macosx-10.5-x86_64-2.7/htslib/bgzf.o build/temp.macosx-10.5-x86_64-2.7/htslib/faidx.o build/temp.macosx-10.5-x86_64-2.7/htslib/hfile.o build/temp.macosx-10.5-x86_64-2.7/htslib/hfile_net.o build/temp.macosx-10.5-x86_64-2.7/htslib/hts.o build/temp.macosx-10.5-x86_64-2.7/htslib/md5.o build/temp.macosx-10.5-x86_64-2.7/htslib/regidx.o build/temp.macosx-10.5-x86_64-2.7/htslib/sam.o build/temp.macosx-10.5-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.macosx-10.5-x86_64-2.7/htslib/vcf_sweep.o build/temp.macosx-10.5-x86_64-2.7/htslib/tbx.o build/temp.macosx-10.5-x86_64-2.7/htslib/vcf.o build/temp.macosx-10.5-x86_64-2.7/htslib/vcfutils.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_decode.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_encode.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_external.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_index.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_io.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/cram_stats.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/files.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/mFILE.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/rANS_static.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/sam_header.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/string_alloc.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/thread_pool.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/vlen.o build/temp.macosx-10.5-x86_64-2.7/htslib/cram/zfio.o build/temp.macosx-10.5-x86_64-2.7/htslib/hfile_libcurl.o -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -lz -lcurl -o build/lib.macosx-10.5-x86_64-2.7/pysam/libchtslib.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libchtslib.so -Wl,-x

skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)

building 'pysam.libcsamfile' extension

creating build/temp.macosx-10.5-x86_64-2.7/samtools

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libcsamfile.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/htslib_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/samfile_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c samtools/kprobaln.c -o build/temp.macosx-10.5-x86_64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libcsamfile.o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o build/temp.macosx-10.5-x86_64-2.7/pysam/samfile_util.o build/temp.macosx-10.5-x86_64-2.7/samtools/kprobaln.o -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -lz -lcurl -lchtslib -o build/lib.macosx-10.5-x86_64-2.7/pysam/libcsamfile.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libcsamfile.so -Wl,-x

cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c

building 'pysam.libcalignmentfile' extension

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libcalignmentfile.c:22757:21: warning: assigning to 'bam_pileup1_t *' from

'const bam_pileup1_t *' discards qualifiers

[-Wincompatible-pointer-types-discards-qualifiers]

...= bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));

^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1 warning generated.

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/htslib_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/samfile_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c samtools/kprobaln.c -o build/temp.macosx-10.5-x86_64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libcalignmentfile.o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o build/temp.macosx-10.5-x86_64-2.7/pysam/samfile_util.o build/temp.macosx-10.5-x86_64-2.7/samtools/kprobaln.o -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -lz -lcurl -lchtslib -o build/lib.macosx-10.5-x86_64-2.7/pysam/libcalignmentfile.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libcalignmentfile.so -Wl,-x

skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)

building 'pysam.libcalignedsegment' extension

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libcalignedsegment.c:3849:32: warning: explicitly assigning value of variable of type

'struct __pyx_obj_5pysam_18libcalignedsegment___pyx_scope_struct__genexpr *' to itself

[-Wself-assign]

if (1); else __pyx_cur_scope = __pyx_cur_scope;

~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~

pysam/libcalignedsegment.c:3999:32: warning: explicitly assigning value of variable of type

'struct __pyx_obj_5pysam_18libcalignedsegment___pyx_scope_struct_1_genexpr *' to

itself [-Wself-assign]

if (1); else __pyx_cur_scope = __pyx_cur_scope;

~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~

2 warnings generated.

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/htslib_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/samfile_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -Isamtools -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c samtools/kprobaln.c -o build/temp.macosx-10.5-x86_64-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libcalignedsegment.o build/temp.macosx-10.5-x86_64-2.7/pysam/htslib_util.o build/temp.macosx-10.5-x86_64-2.7/pysam/samfile_util.o build/temp.macosx-10.5-x86_64-2.7/samtools/kprobaln.o -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -lz -lcurl -lchtslib -o build/lib.macosx-10.5-x86_64-2.7/pysam/libcalignedsegment.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libcalignedsegment.so -Wl,-x

skipping 'pysam/libctabix.c' Cython extension (up-to-date)

building 'pysam.libctabix' extension

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libctabix.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libctabix.c:5970:27: warning: assigning to 'char **' from 'const char **' discards

qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]

__pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));

^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1 warning generated.

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ipysam -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/tabix_util.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/tabix_util.c:20:3: warning: implicitly declaring library function 'memset' with type

'void *(void *, int, unsigned long)'

memset(*line, 0, *linelen);

^

pysam/tabix_util.c:20:3: note: include the header <string.h> or explicitly provide a

declaration for 'memset'

pysam/tabix_util.c:23:11: warning: implicitly declaring library function 'strlen' with type

'unsigned long (const char *)'

return (strlen(*line));

^

pysam/tabix_util.c:23:11: note: include the header <string.h> or explicitly provide a

declaration for 'strlen'

2 warnings generated.

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libctabix.o build/temp.macosx-10.5-x86_64-2.7/pysam/tabix_util.o -Lpysam -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -lz -lcurl -lchtslib -o build/lib.macosx-10.5-x86_64-2.7/pysam/libctabix.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libctabix.so -Wl,-x

skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)

building 'pysam.libctabixproxies' extension

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/gary/anaconda/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libctabixproxies.c:4114:34: warning: comparison of unsigned expression < 0 is always

false [-Wtautological-compare]

__pyx_t_4 = ((__pyx_v_nbytes < 0) != 0);

~~~~~~~~~~~~~~ ^ ~

1 warning generated.

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libctabixproxies.o -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -lz -lcurl -lchtslib -o build/lib.macosx-10.5-x86_64-2.7/pysam/libctabixproxies.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libctabixproxies.so -Wl,-x

skipping 'pysam/libcvcf.c' Cython extension (up-to-date)

building 'pysam.libcvcf' extension

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ihtslib -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libcvcf.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libcvcf.c:26073:32: warning: explicitly assigning value of variable of type 'struct

__pyx_obj_5pysam_7libcvcf___pyx_scope_struct___parse *' to itself [-Wself-assign]

if (1); else __pyx_cur_scope = __pyx_cur_scope;

~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~

1 warning generated.

gcc -undefined dynamic_lookup -L/Users/gary/anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/pysam/libcvcf.o -Lpysam -L. -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -Lbuild/lib.macosx-10.5-x86_64-2.7/pysam -L/Users/gary/anaconda/lib -lz -lcurl -lchtslib -o build/lib.macosx-10.5-x86_64-2.7/pysam/libcvcf.so -dynamiclib -rpath /Users/gary/anaconda/lib/python2.7/site-packages -Wl,-headerpad_max_install_names -Wl,-install_name,@rpath/pysam-0.10.0-py2.7-macosx-10.5-x86_64.egg/pysam/libcvcf.so -Wl,-x

cythoning pysam/libcbcf.pyx to pysam/libcbcf.c

Error compiling Cython file:

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

...

raise TypeError('this class cannot be instantiated from Python')

@property

def name(self):

"""contig name"""

cdef bcf_hdr_t *hdr = self.header.ptr

^

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

pysam/libcbcf.pyx:1542:41: Cannot convert Python object to 'bcf_hdr_t *'

Error compiling Cython file:

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

...

return self.id

@property

def length(self):

"""contig length or None if not available"""

cdef bcf_hdr_t *hdr = self.header.ptr

^

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

pysam/libcbcf.pyx:1553:41: Cannot convert Python object to 'bcf_hdr_t *'

Error compiling Cython file:

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

...

return length if length else None

@property

def header(self):

""":class:`VariantHeaderRecord` associated with this :class:`VariantContig` object"""

cdef bcf_hdr_t *hdr = self.header.ptr

^

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

pysam/libcbcf.pyx:1560:41: Cannot convert Python object to 'bcf_hdr_t *'

Error compiling Cython file:

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

...

cdef bcf_hdr_t *hdr = self.header.ptr

cdef bcf_hrec_t *hrec = hdr.id[BCF_DT_CTG][self.id].val.hrec[0]

return makeVariantHeaderRecord(self.header, hrec)

def remove_header(self):

cdef bcf_hdr_t *hdr = self.header.ptr

^

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

pysam/libcbcf.pyx:1565:41: Cannot convert Python object to 'bcf_hdr_t *'

building 'pysam.libcbcf' extension

gcc -fno-strict-aliasing -I/Users/gary/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ihtslib -I. -Ihtslib -I/Users/gary/anaconda/include/python2.7 -c pysam/libcbcf.c -o build/temp.macosx-10.5-x86_64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libcbcf.c:1:2: error: Do not use this file, it is the result of a failed Cython

compilation.

#error Do not use this file, it is the result of a failed Cython compilation.

^

1 error generated.

error: command 'gcc' failed with exit status 1

gary >

Sebastian Luna Valero

unread,

Mar 23, 2017, 4:46:58 AM3/23/17

to pysam-us...@googlegroups.com

Hello,

Could you please try installing pysam with conda?
http://bioconda.github.io/recipes/pysam/README.html

Best regards,

Sebastian

Yung-Chih Lai

unread,

Mar 23, 2017, 4:58:38 AM3/23/17

to pysam-us...@googlegroups.com

Hi Sebastian,

Thank you so much for your help. I have tried, but it doesn’t work below. By the way, I don’t know why it ask me to downgrade pysam from 0.8.4-py27_0 to 0.6-py27_0. Could you help me again? Many thanks.

Best,

Gary

1. Install pysam using conda

gary > conda install pysam

Fetching package metadata: ....

Solving package specifications: ...................

Package plan for installation in environment /Users/gary/anaconda:

The following packages will be downloaded:

package | build

---------------------------|-----------------

conda-env-2.6.0 | 0 601 B

openssl-1.0.2k | 1 3.0 MB

sqlite-3.13.0 | 0 1.4 MB

zlib-1.2.8 | 3 89 KB

python-2.7.13 | 0 9.1 MB

enum34-1.1.6 | py27_0 54 KB

idna-2.2 | py27_0 121 KB

ipaddress-1.0.18 | py27_0 30 KB

pyasn1-0.2.3 | py27_0 75 KB

pycosat-0.6.2 | py27_0 97 KB

pycparser-2.17 | py27_0 153 KB

pysam-0.6 | py27_0 670 KB

requests-2.13.0 | py27_0 776 KB

ruamel_yaml-0.11.14 | py27_1 197 KB

setuptools-27.2.0 | py27_0 522 KB

cffi-1.9.1 | py27_0 193 KB

pip-9.0.1 | py27_1 1.6 MB

cryptography-1.7.1 | py27_0 468 KB

pyopenssl-16.2.0 | py27_0 68 KB

conda-4.3.14 | py27_0 482 KB

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

Total: 19.0 MB

The following NEW packages will be INSTALLED:

ruamel_yaml: 0.11.14-py27_1

The following packages will be UPDATED:

cffi: 1.2.1-py27_0 --> 1.9.1-py27_0

conda: 3.19.1-py27_0 --> 4.3.14-py27_0

conda-env: 2.4.5-py27_0 --> 2.6.0-0

cryptography: 1.0.2-py27_0 --> 1.7.1-py27_0

enum34: 1.0.4-py27_0 --> 1.1.6-py27_0

idna: 2.0-py27_0 --> 2.2-py27_0

ipaddress: 1.0.14-py27_0 --> 1.0.18-py27_0

openssl: 1.0.2f-0 --> 1.0.2k-1

pip: 8.0.2-py27_0 --> 9.0.1-py27_1

pyasn1: 0.1.9-py27_0 --> 0.2.3-py27_0

pycosat: 0.6.1-py27_0 --> 0.6.2-py27_0

pycparser: 2.14-py27_0 --> 2.17-py27_0

pyopenssl: 0.15.1-py27_1 --> 16.2.0-py27_0

python: 2.7.11-0 --> 2.7.13-0

requests: 2.9.1-py27_0 --> 2.13.0-py27_0

setuptools: 19.6.2-py27_0 --> 27.2.0-py27_0

sqlite: 3.9.2-0 --> 3.13.0-0

zlib: 1.2.8-0 --> 1.2.8-3

The following packages will be DOWNGRADED:

pysam: 0.8.4-py27_0 --> 0.6-py27_0

Proceed ([y]/n)? y

Fetching packages ...

conda-env-2.6. 100% |############################################| Time: 0:00:00 503.75 kB/s

openssl-1.0.2k 100% |############################################| Time: 0:00:00 4.04 MB/s

sqlite-3.13.0- 100% |############################################| Time: 0:00:00 5.56 MB/s

zlib-1.2.8-3.t 100% |############################################| Time: 0:00:00 1.18 MB/s

python-2.7.13- 100% |############################################| Time: 0:00:01 5.12 MB/s

enum34-1.1.6-p 100% |############################################| Time: 0:00:00 878.94 kB/s

idna-2.2-py27_ 100% |############################################| Time: 0:00:00 1.36 MB/s

ipaddress-1.0. 100% |############################################| Time: 0:00:00 953.28 kB/s

pyasn1-0.2.3-p 100% |############################################| Time: 0:00:00 1.08 MB/s

pycosat-0.6.2- 100% |############################################| Time: 0:00:00 1.30 MB/s

pycparser-2.17 100% |############################################| Time: 0:00:00 1.57 MB/s

pysam-0.6-py27 100% |############################################| Time: 0:00:00 2.36 MB/s

requests-2.13. 100% |############################################| Time: 0:00:00 813.33 kB/s

ruamel_yaml-0. 100% |############################################| Time: 0:00:00 1.46 MB/s

setuptools-27. 100% |############################################| Time: 0:00:00 1.91 MB/s

cffi-1.9.1-py2 100% |############################################| Time: 0:00:00 1.69 MB/s

pip-9.0.1-py27 100% |############################################| Time: 0:00:00 4.17 MB/s

cryptography-1 100% |############################################| Time: 0:00:00 2.40 MB/s

pyopenssl-16.2 100% |############################################| Time: 0:00:00 1.01 MB/s

conda-4.3.14-p 100% |############################################| Time: 0:00:00 870.29 kB/s

Extracting packages ...

[ COMPLETE ]|###############################################################| 100%

Unlinking packages ...

[ COMPLETE ]|###############################################################| 100%

Linking packages ...

2. htseq-count still cannot find pysam

gary > ls

BamToSamToHTSeq.txt L_FE9D_R570.txt

Chuong569.bam L_FE9D_R571.txt

Chuong569_bam.txt galGal4UCSCensGene81_TableBrowser.gtf

L_FE9D_R569.txt

gary > htseq-count -f bam -s no -a 10 -t exon -i gene_id -m union Chuong569.bam galGal4UCSCensGene81_TableBrowser.gtf > Chuong569_bam.txt

100000 GFF lines processed.

200000 GFF lines processed.

300000 GFF lines processed.

386159 GFF lines processed.

Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/)Error occured when reading beginning of SAM/BAM file.

No module named pysam

[Exception type: ImportError, raised in __init__.py:937]

gary > which PySam

gary > which pysam

gary >

--
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For more options, visit https://groups.google.com/d/optout.

Sebastian Luna Valero

unread,

Mar 23, 2017, 6:01:09 AM3/23/17

to pysam-us...@googlegroups.com

Hello,

On Mac OS X, I am afraid that the latest available version of pysam in bioconda is 0.6. Below are the steps that I have followed:
curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh -b -p /Users/sebastian/conda/i1
export PATH=/Users/sebastian/conda/i1/bin:$PATH
conda create -n pysam pysam
source activate pysam
python -c "import pysam"

If you want the latest pysam version, you can either use docker containers on Mac OS X as explained here:
http://bioconda.github.io/recipes/pysam/README.html

or go to a Linux system with conda.

Best regards,

Sebastian

Marcel Martin

unread,

Mar 23, 2017, 7:54:19 AM3/23/17

to pysam-us...@googlegroups.com

On 2017-03-23 11:01, Sebastian Luna Valero wrote:
> On Mac OS X, I am afraid that the latest available version of pysam in
> bioconda is 0.6. Below are the steps that I have followed:

Hm, according to https://anaconda.org/bioconda/pysam/files , there
exists a "osx-64/pysam-0.10.0-py27_3.tar.bz2" file. So pysam 0.10.0
should be available.

On 2017-03-23 09:58, Yung-Chih Lai wrote:
> Thank you so much for your help. I have tried, but it doesn’t work
> below. By the way, I don’t know why it ask me to downgrade pysam from
> 0.8.4-py27_0 to 0.6-py27_0. Could you help me again? Many thanks.

Did you add the bioconda channels to the conda channel list?

You need to follow these instructions:
https://bioconda.github.io/#set-up-channels

When you have done that, just install HTSeq directly with 'conda install
htseq', and it will automatically install pysam as a dependency.

Marcel

Sebastian Luna Valero

unread,

Mar 23, 2017, 10:11:33 AM3/23/17

to pysam-us...@googlegroups.com

Hello,

You are absolutely right. Sorry for missing that step!

Here is the complete list of instructions:

curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh -b -p /Users/sebastian/conda/i1
export PATH=/Users/sebastian/conda/i1/bin:$PATH

conda config --add channels 'conda-forge'
conda config --add channels 'defaults'
conda config --add channels 'r'
conda config --add channels 'bioconda'

conda create -n pysam pysam
source activate pysam
python -c "import pysam"

Now you should have the latest pysam version installed.

Best regards,

Sebastian

Yung-Chih Lai

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Mar 24, 2017, 1:06:30 AM3/24/17

to pysam-us...@googlegroups.com

Hi Sebastian & Marcel,

Many thanks for your help. I installed pysam based on Sebastian’s command lines, but it didn’t work. Both of two tools, i.e. htseq-count & HiC-Pro, still cannot work on my MacBook Pro notebook, because of pysam. Please see the detail below. What I did is wrong? Could you help me again? Many thanks.

Best,

Gary

# Installation of pysam

gary > pwd

/Users/gary/Applications

gary > ls

Aspera Connect.app/ bedGraphToBigWig

Aspera Crypt.app/ bedSort

CEAS-Package-1.0.2/ bedToBigBed

Chrome Apps.localized/ bigWigToBedGraph

Flux.app/ bowtie2-2.3.0/

HTSeq-0.6.1/ fetchChromSizes

HiC-Pro-master/ genePredToGtf

HiC-Pro_2.8.1_devel/ hgWiggle

ROSE/ homer/

Trimmomatic-0.36/ mafSplit

Utilities/ pysam-0.10.0/

Wineskin/ qualimap-build-24-09-15/

Wineskin Winery.app/ rar/

axtToMaf sratoolkit.2.8.1-2-mac64/

bamUtil/ weblogo/

bedClip wigToBigWig

gary > rm -fr pysam-0.10.0/

gary > pwd

/Users/gary/Applications

gary > ls

Aspera Connect.app/ bedGraphToBigWig

Aspera Crypt.app/ bedSort

CEAS-Package-1.0.2/ bedToBigBed

Chrome Apps.localized/ bigWigToBedGraph

Flux.app/ bowtie2-2.3.0/

HTSeq-0.6.1/ fetchChromSizes

HiC-Pro-master/ genePredToGtf

HiC-Pro_2.8.1_devel/ hgWiggle

ROSE/ homer/

Trimmomatic-0.36/ mafSplit

Utilities/ qualimap-build-24-09-15/

Wineskin/ rar/

Wineskin Winery.app/ sratoolkit.2.8.1-2-mac64/

axtToMaf weblogo/

bamUtil/ wigToBigWig

bedClip

gary > curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

% Total % Received % Xferd Average Speed Time Time Time Current

Dload Upload Total Spent Left Speed

100 24.0M 100 24.0M 0 0 3494k 0 0:00:07 0:00:07 --:--:-- 8577k

gary > ll

total 81784

drwxrwxr-x 3 gary staff 102B Feb 7 04:47 Aspera Connect.app/

drwxrwxr-x 3 gary staff 102B Feb 7 04:47 Aspera Crypt.app/

drwxr-xr-x@ 10 gary staff 340B Feb 1 2016 CEAS-Package-1.0.2/

drwx------@ 10 gary staff 340B Jan 29 2016 Chrome Apps.localized/

drwxr-xr-x 3 gary staff 102B Sep 6 2016 Flux.app/

drwxr-xr-x@ 15 gary staff 510B Aug 17 2015 HTSeq-0.6.1/

drwxr-xr-x@ 19 gary staff 646B Mar 11 16:34 HiC-Pro-master/

drwxr-xr-x@ 19 gary staff 646B Mar 11 16:34 HiC-Pro_2.8.1_devel/

-rw-r--r-- 1 gary staff 24M Mar 24 12:41 Miniconda3-latest-MacOSX-x86_64.sh

drwxrwxrwx 13 gary staff 442B Nov 30 04:25 ROSE/

drwxr-xr-x@ 6 gary staff 204B Mar 13 04:08 Trimmomatic-0.36/

drwxr-xr-x 3 gary staff 102B Dec 3 2015 Utilities/

drwxr-xr-x 4 gary staff 136B Aug 22 2015 Wineskin/

drwxr-xr-x@ 3 gary staff 102B Aug 4 2012 Wineskin Winery.app/

-rwxrwxrwx@ 1 gary staff 483K Nov 28 2015 axtToMaf

drwxr-xr-x 4 gary staff 136B May 9 2016 bamUtil/

-rwx------@ 1 gary staff 460K Sep 7 2015 bedClip

-rwxrwxrwx@ 1 gary staff 466K Nov 29 2015 bedGraphToBigWig

-rwxrwxrwx@ 1 gary staff 581K Jun 28 2016 bedSort

-rwxrwxrwx@ 1 gary staff 607K Feb 10 2016 bedToBigBed

-rwxr-xr-x@ 1 gary staff 461K Mar 31 2016 bigWigToBedGraph

drwxr-xr-x@ 28 gary staff 952B Feb 18 22:43 bowtie2-2.3.0/

-rwxrwxrwx@ 1 gary staff 2.6K Feb 4 2016 fetchChromSizes

-rwxrwxrwx@ 1 gary staff 6.0M Nov 20 2015 genePredToGtf

-rwxrwxrwx@ 1 gary staff 5.9M Dec 30 2015 hgWiggle

drwxr-xr-x 15 gary staff 510B Dec 21 04:43 homer/

-rwxrwxrwx@ 1 gary staff 585K Nov 28 2015 mafSplit

drwxr-xr-x@ 16 gary staff 544B Oct 4 2015 qualimap-build-24-09-15/

drwxr-xr-x@ 12 gary staff 408B Aug 11 2015 rar/

drwxr-xr-x@ 10 gary staff 340B Feb 7 02:51 sratoolkit.2.8.1-2-mac64/

drwxr-xr-x@ 25 gary staff 850B Dec 20 08:15 weblogo/

-rwxrwxrwx@ 1 gary staff 476K Feb 4 2016 wigToBigWig

gary > bash Miniconda3-latest-MacOSX-x86_64.sh -b -p /Users/gary/anaconda/i1

PREFIX=/Users/gary/anaconda/i1

installing: python-3.6.0-0 ...

installing: cffi-1.9.1-py36_0 ...

installing: conda-env-2.6.0-0 ...

installing: cryptography-1.7.1-py36_0 ...

installing: idna-2.2-py36_0 ...

installing: openssl-1.0.2k-0 ...

installing: pyasn1-0.1.9-py36_0 ...

installing: pycosat-0.6.1-py36_1 ...

installing: pycparser-2.17-py36_0 ...

installing: pyopenssl-16.2.0-py36_0 ...

installing: readline-6.2-2 ...

installing: requests-2.12.4-py36_0 ...

installing: ruamel_yaml-0.11.14-py36_1 ...

installing: setuptools-27.2.0-py36_0 ...

installing: six-1.10.0-py36_0 ...

installing: sqlite-3.13.0-0 ...

installing: tk-8.5.18-0 ...

installing: xz-5.2.2-1 ...

installing: yaml-0.1.6-0 ...

installing: zlib-1.2.8-3 ...

installing: conda-4.3.11-py36_0 ...

installing: pip-9.0.1-py36_1 ...

installing: wheel-0.29.0-py36_0 ...

Python 3.6.0 :: Continuum Analytics, Inc.

creating default environment...

installation finished.

WARNING:

You currently have a PYTHONPATH environment variable set. This may cause

unexpected behavior when running the Python interpreter in Miniconda3.

For best results, please verify that your PYTHONPATH only points to

directories of packages that are compatible with the Python interpreter

in Miniconda3: /Users/gary/anaconda/i1

gary > export PATH=/Users/gary/anaconda/i1/bin:$PATH

gary > conda config --add channels 'conda-forge'

gary > conda config --add channels 'defaults'

Warning: 'defaults' already in 'channels' list, moving to the top

gary > conda config --add channels 'r'

gary > conda config --add channels 'bioconda'

gary > conda create -n pysam pysam

Fetching package metadata ...............

Solving package specifications: .

Package plan for installation in environment /Users/gary/anaconda/i1/envs/pysam:

The following NEW packages will be INSTALLED:

bcftools: 1.3.1-1 bioconda

curl: 7.52.1-0

htslib: 1.3.2-0 bioconda

openssl: 1.0.2k-1

pip: 9.0.1-py35_1

pysam: 0.10.0-py35_3 bioconda

python: 3.5.3-1

readline: 6.2-2

samtools: 1.3.1-5 bioconda

setuptools: 27.2.0-py35_0

sqlite: 3.13.0-0

tk: 8.5.18-0

wheel: 0.29.0-py35_0

xz: 5.2.2-1

zlib: 1.2.8-3

Proceed ([y]/n)? y

openssl-1.0.2k 100% |############################################| Time: 0:00:00 5.54 MB/s

readline-6.2-2 100% |############################################| Time: 0:00:00 10.80 MB/s

sqlite-3.13.0- 100% |############################################| Time: 0:00:00 11.28 MB/s

tk-8.5.18-0.ta 100% |############################################| Time: 0:00:00 10.39 MB/s

xz-5.2.2-1.tar 100% |############################################| Time: 0:00:00 10.85 MB/s

zlib-1.2.8-3.t 100% |############################################| Time: 0:00:00 14.70 MB/s

bcftools-1.3.1 100% |############################################| Time: 0:00:05 119.56 kB/s

curl-7.52.1-0. 100% |############################################| Time: 0:00:00 11.83 MB/s

python-3.5.3-1 100% |############################################| Time: 0:00:01 6.92 MB/s

htslib-1.3.2-0 100% |############################################| Time: 0:00:03 292.31 kB/s

samtools-1.3.1 100% |############################################| Time: 0:00:01 303.46 kB/s

setuptools-27. 100% |############################################| Time: 0:00:00 4.73 MB/s

wheel-0.29.0-p 100% |############################################| Time: 0:00:00 7.68 MB/s

pip-9.0.1-py35 100% |############################################| Time: 0:00:00 5.66 MB/s

pysam-0.10.0-p 100% |############################################| Time: 0:00:04 363.23 kB/s

#

# To activate this environment, use:

# > source activate pysam

#

# To deactivate this environment, use:

# > source deactivate pysam

#

gary > source activate pysam

(pysam) gary > python -c "import pysam"

(pysam) gary > exit

logout

[Process completed]

# htseq-count cannot work becasue of pysam

gary > pwd

/Users/gary/Downloads/htseq

gary > ll

total 2075280

-rwxr-xr-x@ 1 gary staff 966M Mar 14 08:41 Chuong569.bam

-rw-r--r--@ 1 gary staff 47M Mar 3 10:40 galGal4UCSCensGene81_TableBrowser.gtf

gary > htseq-count -f bam -s no -a 10 -t exon -i gene_id -m union Chuong569.bam galGal4UCSCensGene81_TableBrowser.gtf > Chuong569_bam.txt

100000 GFF lines processed.

200000 GFF lines processed.

300000 GFF lines processed.

386159 GFF lines processed.

Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/)Error occured when reading beginning of SAM/BAM file.

No module named pysam

[Exception type: ImportError, raised in __init__.py:937]

gary >

#HiC-Pro cannot work becasue of pysam

gary > pwd

/Users/gary/Downloads/HiCPro_testdata

gary > ll

total 8

-rw-r--r--@ 1 gary staff 2.7K Mar 13 19:23 config_test_latest.txt

drwx------@ 9 gary staff 306B Mar 13 11:36 hg19/

drwxr-xr-x@ 5 gary staff 170B Mar 13 09:52 test_data/

gary > HiC-Pro -i test_data/ -o hicpro_latest_test -c config_test_latest.txt

Run HiC-Pro 2.8.1_devel

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

Fri Mar 24 12:54:44 CST 2017

Bowtie2 alignment step1 ...

/Users/gary/Applications/HiC-Pro_2.8.1_devel/scripts/bowtie_wrap.sh -c /Users/gary/Downloads/HiCPro_testdata/config_test_latest.txt -u >> hicpro.log

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

Fri Mar 24 12:55:10 CST 2017

Bowtie2 alignment step2 ...

/Users/gary/Applications/HiC-Pro_2.8.1_devel/scripts/bowtie_wrap.sh -c /Users/gary/Downloads/HiCPro_testdata/config_test_latest.txt -l >> hicpro.log

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

Fri Mar 24 12:55:19 CST 2017

Combine both alignment ...

/Users/gary/Applications/HiC-Pro_2.8.1_devel/scripts/bowtie_combine.sh -c /Users/gary/Downloads/HiCPro_testdata/config_test_latest.txt >> hicpro.log

Usage: samtools sort [options...] [in.bam]

Options:

-l INT Set compression level, from 0 (uncompressed) to 9 (best)

-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]

-n Sort by read name

-o FILE Write final output to FILE rather than standard output

-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or

-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)

-@ INT Set number of sorting and compression threads [1]

Legacy usage: samtools sort [options...] <in.bam> <out.prefix>

Options:

-f Use <out.prefix> as full final filename rather than prefix

-o Write final output to stdout rather than <out.prefix>.bam

-l,m,n,@ Similar to corresponding options above

Usage: samtools sort [options...] [in.bam]

Options:

-l INT Set compression level, from 0 (uncompressed) to 9 (best)

-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]

-n Sort by read name

-o FILE Write final output to FILE rather than standard output

-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or

-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)

-@ INT Set number of sorting and compression threads [1]

Legacy usage: samtools sort [options...] <in.bam> <out.prefix>

Options:

-f Use <out.prefix> as full final filename rather than prefix

-o Write final output to stdout rather than <out.prefix>.bam

-l,m,n,@ Similar to corresponding options above

Usage: samtools sort [options...] [in.bam]

Options:

-l INT Set compression level, from 0 (uncompressed) to 9 (best)

-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]

-n Sort by read name

-o FILE Write final output to FILE rather than standard output

-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or

-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)

-@ INT Set number of sorting and compression threads [1]

Legacy usage: samtools sort [options...] <in.bam> <out.prefix>

Options:

-f Use <out.prefix> as full final filename rather than prefix

-o Write final output to stdout rather than <out.prefix>.bam

-l,m,n,@ Similar to corresponding options above

Usage: samtools sort [options...] [in.bam]

Options:

-l INT Set compression level, from 0 (uncompressed) to 9 (best)

-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]

-n Sort by read name

-o FILE Write final output to FILE rather than standard output

-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or

-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)

-@ INT Set number of sorting and compression threads [1]

Legacy usage: samtools sort [options...] <in.bam> <out.prefix>

Options:

-f Use <out.prefix> as full final filename rather than prefix

-o Write final output to stdout rather than <out.prefix>.bam

-l,m,n,@ Similar to corresponding options above

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

Fri Mar 24 12:55:21 CST 2017

Bowtie2 mapping statistics for R1 and R2 tags ...

/Users/gary/Applications/HiC-Pro_2.8.1_devel/scripts/mapping_stat.sh -c /Users/gary/Downloads/HiCPro_testdata/config_test_latest.txt >> hicpro.log

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

Fri Mar 24 12:55:22 CST 2017

Pairing of R1 and R2 tags ...

/Users/gary/Applications/HiC-Pro_2.8.1_devel/scripts/bowtie_pairing.sh -c /Users/gary/Downloads/HiCPro_testdata/config_test_latest.txt >> hicpro.log

Traceback (most recent call last):

File "/Users/gary/Applications/HiC-Pro_2.8.1_devel/scripts/mergeSAM.py", line 21, in <module>

import pysam

File "/Users/gary/anaconda/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>

from csamtools import *

File "pysam/csamtools.pyx", line 1, in init pysam.csamtools (pysam/csamtools.c:5722)

ImportError: No module named cutils

make: *** [bowtie_pairing] Error 1

gary >

Marcel Martin

unread,

Mar 24, 2017, 4:44:16 AM3/24/17

to pysam-us...@googlegroups.com

On 2017-03-24 06:06, Yung-Chih Lai wrote:
> Many thanks for your help. I installed pysam based on Sebastian’s
> command lines, but it didn’t work. Both of two tools, i.e. htseq-count &
> HiC-Pro, still cannot work on my MacBook Pro notebook, because of pysam.
> Please see the detail below. What I did is wrong? Could you help me
> again? Many thanks.

My suggestion is to not use the manually downloaded htseq, but to use
the package from bioconda instead. You do that by running 'conda install
htseq'. Then make sure that the command 'which htseq-count' shows the
path to the Conda version of the binary, and not the path to your
manually installed one.

Marcel

Yung-Chih Lai

unread,

Mar 24, 2017, 5:22:42 AM3/24/17

to pysam-us...@googlegroups.com

Hi Marcel,

Many thanks for your help. I will try it. May I know that, after installing htseq using conda, whether other tools, e.g. HiC-Pro also can find pysam on my Mac, or not? Now, without pysam, I still can run htseq-count to quantify sam files, but I totally cannot run HiC-Pro. Or I also can use conda to install HiC-Pro? Thanks a lot.

Best,

Gary

Marcel Martin

unread,

Mar 24, 2017, 5:55:21 AM3/24/17

to pysam-us...@googlegroups.com

On 2017-03-24 10:22, Yung-Chih Lai wrote:
> Many thanks for your help. I will try it. May I know that, after
> installing htseq using conda, whether other tools, e.g. HiC-Pro also can
> find pysam on my Mac, or not? Now, without pysam, I still can run
> htseq-count to quantify sam files, but I totally cannot run HiC-Pro. Or
> I also can use conda to install HiC-Pro? Thanks a lot.

Hi, it seems that HiC-Pro is not available on bioconda, which makes it a
bit more difficult. But it should be possible to use HiC-Pro with a
pysam installed from bioconda.

Two suggestions:

* You need to make sure that you the "pysam" environment is activated
before you run HiC-Pro.

* Unset PYTHONPATH (as suggested by miniconda install)

Also, note that the Python versions between programs and their
dependencies need to match: If htseq-count runs under Python 2.7, then
pysam for Python 2.7 needs to be installed. "conda install"
automatically takes care of this, but if you run HiC-Pro, then you need
to watch this yourself. So possibly you need to create a new environment
with the commands Sebastian listed, but by also specifying that you want
Python 2:

conda create -n pysam-py2 pysam python=2

Then you would need to activate pysam-py2 (instead of pysam) in the
future if you want to use it:

source activate pysam-py2

It would be a good idea to get a local person to help you because these
things are hard to figure out remotely.

Marcel

Yung-Chih Lai

unread,

Mar 25, 2017, 5:03:41 AM3/25/17

to pysam-us...@googlegroups.com

Hi Marcel,

Thank you so much for your help. However, I don't fully understand your suggestions. Could you provide some web links with basic information about pysam environment, PYTHONPATH, and conda that I can learn by myself? Of course, I will try to find a local person who can help me. Thanks again.

Best,

Gary

Marcel

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