search

cgat-developers / cgat-apps

cgat-apps repository
Other
33 stars 14 forks source link

Error with cgat bam2stats (ImportError: libhts.so.2: cannot open shared object file: No such file or directory) #82

Closed lucygarner closed 3 years ago

lucygarner commented 3 years ago

Hi,

I installed cgat-apps using Conda. When I run cgat --help this works as expected, however when I run cgat bam2stats --help, I get the following error:

File "/user/lucy/conda-install/envs/rna-seq_2021/lib/python3.6/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * ImportError: libhts.so.2: cannot open shared object file: No such file or directory

This occurs even in a fresh Conda environment where I explicitly installed only cgat-apps and the error is not specific to bam2stats.

Any thoughts on what might be causing this issue?

Best wishes, Lucy

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
aiohttp                   3.7.4            py36h8f6f2f9_0    conda-forge
alignlib-lite             0.3              py36h9f6a78e_4    bioconda
apsw                      3.34.0.r1        py36hb6bac25_0    conda-forge
async-timeout             3.0.1                   py_1000    conda-forge
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
bcftools                  1.8                  h4da6232_3    bioconda
bcrypt                    3.2.0            py36h8f6f2f9_1    conda-forge
bedtools                  2.30.0               h7d7f7ad_1    bioconda
biopython                 1.78             py36h8f6f2f9_2    conda-forge
boto3                     1.17.51            pyhd8ed1ab_0    conda-forge
botocore                  1.20.51            pyhd8ed1ab_0    conda-forge
brotlipy                  0.7.0           py36h8f6f2f9_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2020.12.5            ha878542_0    conda-forge
cachetools                4.2.1              pyhd8ed1ab_0    conda-forge
certifi                   2020.12.5        py36h5fab9bb_1    conda-forge
cffi                      1.14.5           py36hc120d54_0    conda-forge
cgat-apps                 0.6.0            py36h448cc22_1    bioconda
cgatcore                  0.6.7                      py_0    bioconda
chardet                   4.0.0            py36h5fab9bb_1    conda-forge
coreutils                 8.25                          1    bioconda
cryptography              3.4.7            py36hb60f036_0    conda-forge
curl                      7.76.0               h979ede3_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
drmaa                     0.7.9                   py_1000    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
ftputil                   3.2                      py36_0    bioconda
future                    0.18.2           py36h5fab9bb_3    conda-forge
gevent                    1.1rc4                   py36_0    bioconda
google-api-core           1.26.2             pyhd8ed1ab_0    conda-forge
google-auth               1.28.0             pyh44b312d_0    conda-forge
google-cloud-core         1.5.0              pyhd3deb0d_0    conda-forge
google-cloud-sdk          336.0.0          py36h5fab9bb_0    conda-forge
google-cloud-storage      1.19.0                     py_0    conda-forge
google-crc32c             1.1.2            py36h0208b43_0    conda-forge
google-resumable-media    1.2.0              pyhd3deb0d_0    conda-forge
googleapis-common-protos  1.53.0           py36h5fab9bb_0    conda-forge
greenlet                  1.0.0            py36hc4f0c31_0    conda-forge
grep                      3.4                  h9d02d08_1    bioconda
grpcio                    1.37.0           py36h8e87921_0    conda-forge
htslib                    1.7                           0    bioconda
idna                      2.10               pyh9f0ad1d_0    conda-forge
idna_ssl                  1.1.0           py36h9f0ad1d_1001    conda-forge
importlib-metadata        3.10.1           py36h5fab9bb_0    conda-forge
jmespath                  0.10.0             pyh9f0ad1d_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
kiwisolver                1.3.1            py36h605e78d_1    conda-forge
krb5                      1.17.2               h926e7f8_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
libblas                   3.9.0                8_openblas    conda-forge
libcblas                  3.9.0                8_openblas    conda-forge
libcrc32c                 1.1.1                h9c3ff4c_2    conda-forge
libcurl                   7.76.0               hc4aaa36_0    conda-forge
libdeflate                1.2                  h516909a_1    bioconda
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_19    conda-forge
libgfortran-ng            9.3.0               hff62375_19    conda-forge
libgfortran5              9.3.0               hff62375_19    conda-forge
libgomp                   9.3.0               h2828fa1_19    conda-forge
liblapack                 3.9.0                8_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.12          pthreads_h4812303_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libprotobuf               3.15.8               h780b84a_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libtiff                   4.2.0                hdc55705_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
matplotlib-base           3.3.4            py36hd391965_0    conda-forge
multidict                 5.1.0            py36h8f6f2f9_1    conda-forge
mysql-connector-c         6.1.6                         2    bioconda
ncurses                   6.2                  h58526e2_4    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
numpy                     1.19.5           py36h2aa4a07_1    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hf7af979_0    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
packaging                 20.9               pyh44b312d_0    conda-forge
pandas                    1.1.5            py36h284efc9_0    conda-forge
paramiko                  2.7.2              pyh9f0ad1d_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pillow                    8.1.2            py36ha6010c0_1    conda-forge
pip                       21.0.1             pyhd8ed1ab_0    conda-forge
protobuf                  3.15.8           py36hc4f0c31_0    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pybedtools                0.7.10           py36ha92aebf_3    bioconda
pybigwig                  0.3.18           py36h0c3496a_1    bioconda
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pynacl                    1.4.0            py36h8f6f2f9_2    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pysam                     0.14.1           py36hae42fb6_1    bioconda
pysftp                    0.2.9                    py36_0    bioconda
pysocks                   1.7.1            py36h5fab9bb_3    conda-forge
python                    3.6.13          hffdb5ce_0_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-lzo                1.12            py36hbaba66d_1003    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py36h8f6f2f9_0    conda-forge
quicksect                 0.2.2            py36hc5360cc_4    bioconda
readline                  8.0                  he28a2e2_2    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
rsa                       3.1.4                    py36_0    bioconda
ruffus                    2.8.4              pyh864c0ab_1    bioconda
s3transfer                0.3.7              pyhd8ed1ab_0    conda-forge
samtools                  1.7                           1    bioconda
scipy                     1.5.3            py36h9e8f40b_0    conda-forge
setuptools                49.6.0           py36h5fab9bb_3    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sortedcontainers          2.3.0              pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.7            py36h8f6f2f9_0    conda-forge
sqlite                    3.35.4               h74cdb3f_0    conda-forge
time                      1.8                  h516909a_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
tornado                   6.1              py36h8f6f2f9_1    conda-forge
typing-extensions         3.7.4.3                       0    conda-forge
typing_extensions         3.7.4.3                    py_0    conda-forge
ucsc-bedgraphtobigwig     357                           1    bioconda
ucsc-bedtobigbed          357                           1    bioconda
ucsc-wigtobigwig          357                           1    bioconda
urllib3                   1.26.4             pyhd8ed1ab_0    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
yarl                      1.6.3            py36h8f6f2f9_1    conda-forge
zipp                      3.4.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge
Acribbs commented 3 years ago

This is a pysam build error and likely related to the installation of pysam 0.14.1. Can you try conda install pysam=0.15.2

Acribbs commented 3 years ago

You could also try pip uninstall pysam and then pip install pysam=0.15.2

lucygarner commented 3 years ago

Thanks, this seems to have fixed the issue. I had previously tried conda update pysam and this didn't work - must have updated to the wrong version?