lpantano
commented
7 years ago Hi,
Can you look at this to see if that helps:
https://github.com/chapmanb/bcbio-nextgen/issues/1905 https://github.com/chapmanb/bcbio-nextgen/issues/1905
Let me know!
On May 7, 2017, at 2:27 AM, YangZituo notifications@github.com wrote:
Hi, I have already installed the bcbio and run the cutadapt. After i run the collapse, it cannot work.
[ns_phd06@tll-rv1 bin]$ seqcluster collapse -f /data/GenhuaLab/zituo/BCBIOresults/sm0h_1.fastq -o /data/GenhuaLab/zituo/BCBIOresults/sm0h_1.collapser.fastq
Traceback (most recent call last): File "./seqcluster", line 11, in load_entry_point('seqcluster==1.2.4a0', 'console_scripts', 'seqcluster')() File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 565, in load_entry_point File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 2598, in load_entry_point File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 2258, in load File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 2264, in resolve File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/seqcluster/command_line.py", line 5, in from make_clusters import cluster File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/seqcluster/make_clusters.py", line 11, in import pybedtools File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/init.py", line 12, in from . import contrib File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/contrib/init.py", line 3, in from . import venn_maker File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/contrib/venn_maker.py", line 12, in from pybedtools import helpers File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/helpers.py", line 13, in import pysam File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * ImportError: libhts.so.1: cannot open shared object file: No such file or directory
Please help me, Thank!! @lpantano https://github.com/lpantano — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/24, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HPQVyXkHZjCjuclFq_yqbGuiDdWAks5r3WRggaJpZM4NTCDa.
Hi, I have already installed the bcbio and run the cutadapt. After i run the collapse, it cannot work.
[ns_phd06@tll-rv1 bin]$ seqcluster collapse -f /data/GenhuaLab/zituo/BCBIOresults/sm0h_1.fastq -o /data/GenhuaLab/zituo/BCBIOresults/sm0h_1.collapser.fastq
Traceback (most recent call last): File "./seqcluster", line 11, in
load_entry_point('seqcluster==1.2.4a0', 'console_scripts', 'seqcluster')()
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 565, in load_entry_point
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 2598, in load_entry_point
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 2258, in load
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 2264, in resolve
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/seqcluster/command_line.py", line 5, in
from make_clusters import cluster
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/seqcluster/make_clusters.py", line 11, in
import pybedtools
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/init.py", line 12, in
from . import contrib
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/contrib/init.py", line 3, in
from . import venn_maker
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/contrib/venn_maker.py", line 12, in
from pybedtools import helpers
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pybedtools/helpers.py", line 13, in
import pysam
File "/data/GenhuaLab/zituo/local/share/bcbio/anaconda/lib/python2.7/site-packages/pysam/init.py", line 5, in
from pysam.libchtslib import *
ImportError: libhts.so.1: cannot open shared object file: No such file or directory
Please help me, Thank!! @lpantano