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bcbio-variation-recall ensemble error: java.io.IOException: Transport endpoint is not connected #25

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SusanneBioinfo opened this issue Nov 2, 2020 · 0 comments
Open

bcbio-variation-recall ensemble error: java.io.IOException: Transport endpoint is not connected #25

SusanneBioinfo opened this issue Nov 2, 2020 · 0 comments

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@SusanneBioinfo
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SusanneBioinfo commented Nov 2, 2020 •
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Hi!
I run "bcbio-variation-recall ensemble --help" (or any other bcbio-variation-recall command) and get this error message:

Exception in thread "main" java.lang.ExceptionInInitializerError
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at clojure.lang.RT.classForName(RT.java:2207)
at clojure.lang.RT.classForName(RT.java:2216)
at clojure.lang.RT.loadClassForName(RT.java:2235)
at clojure.lang.RT.load(RT.java:453)
at clojure.lang.RT.load(RT.java:428)
at clojure.core$load$fn__6824.invoke(core.clj:6126)
at clojure.core$load.invokeStatic(core.clj:6125)
at clojure.core$load.doInvoke(core.clj:6109)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.core$load_one.invokeStatic(core.clj:5908)
at clojure.core$load_one.invoke(core.clj:5903)
at clojure.core$load_lib$fn__6765.invoke(core.clj:5948)
at clojure.core$load_lib.invokeStatic(core.clj:5947)
at clojure.core$load_lib.doInvoke(core.clj:5928)
at clojure.lang.RestFn.applyTo(RestFn.java:142)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$load_libs.invokeStatic(core.clj:5985)
at clojure.core$load_libs.doInvoke(core.clj:5969)
at clojure.lang.RestFn.applyTo(RestFn.java:137)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$require.invokeStatic(core.clj:6007)
at clojure.core$require.doInvoke(core.clj:6007)
at clojure.lang.RestFn.invoke(RestFn.java:436)
at bcbio.run.fsp$loading__6706__auto____175.invoke(fsp.clj:1)
at bcbio.run.fsp__init.load(Unknown Source)
at bcbio.run.fsp__init.(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at clojure.lang.RT.classForName(RT.java:2207)
at clojure.lang.RT.classForName(RT.java:2216)
at clojure.lang.RT.loadClassForName(RT.java:2235)
at clojure.lang.RT.load(RT.java:453)
at clojure.lang.RT.load(RT.java:428)
at clojure.core$load$fn__6824.invoke(core.clj:6126)
at clojure.core$load.invokeStatic(core.clj:6125)
at clojure.core$load.doInvoke(core.clj:6109)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.core$load_one.invokeStatic(core.clj:5908)
at clojure.core$load_one.invoke(core.clj:5903)
at clojure.core$load_lib$fn__6765.invoke(core.clj:5948)
at clojure.core$load_lib.invokeStatic(core.clj:5947)
at clojure.core$load_lib.doInvoke(core.clj:5928)
at clojure.lang.RestFn.applyTo(RestFn.java:142)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$load_libs.invokeStatic(core.clj:5985)
at clojure.core$load_libs.doInvoke(core.clj:5969)
at clojure.lang.RestFn.applyTo(RestFn.java:137)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$require.invokeStatic(core.clj:6007)
at clojure.core$require.doInvoke(core.clj:6007)
at clojure.lang.RestFn.invoke(RestFn.java:1289)
at bcbio.variation.recall.merge$loading__6706__auto____173.invoke(merge.clj:1)
at bcbio.variation.recall.merge__init.load(Unknown Source)
at bcbio.variation.recall.merge__init.(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at clojure.lang.RT.classForName(RT.java:2207)
at clojure.lang.RT.classForName(RT.java:2216)
at clojure.lang.RT.loadClassForName(RT.java:2235)
at clojure.lang.RT.load(RT.java:453)
at clojure.lang.RT.load(RT.java:428)
at clojure.core$load$fn__6824.invoke(core.clj:6126)
at clojure.core$load.invokeStatic(core.clj:6125)
at clojure.core$load.doInvoke(core.clj:6109)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.core$load_one.invokeStatic(core.clj:5908)
at clojure.core$load_one.invoke(core.clj:5903)
at clojure.core$load_lib$fn__6765.invoke(core.clj:5948)
at clojure.core$load_lib.invokeStatic(core.clj:5947)
at clojure.core$load_lib.doInvoke(core.clj:5928)
at clojure.lang.RestFn.applyTo(RestFn.java:142)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$load_libs.invokeStatic(core.clj:5985)
at clojure.core$load_libs.doInvoke(core.clj:5969)
at clojure.lang.RestFn.applyTo(RestFn.java:137)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$require.invokeStatic(core.clj:6007)
at clojure.core$require.doInvoke(core.clj:6007)
at clojure.lang.RestFn.invoke(RestFn.java:482)
at bcbio.variation.recall.main$loading__6706__auto____171.invoke(main.clj:1)
at bcbio.variation.recall.main__init.load(Unknown Source)
at bcbio.variation.recall.main__init.(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at clojure.lang.RT.classForName(RT.java:2207)
at clojure.lang.RT.classForName(RT.java:2216)
at clojure.lang.RT.loadClassForName(RT.java:2235)
at clojure.lang.RT.load(RT.java:453)
at clojure.lang.RT.load(RT.java:428)
at clojure.core$load$fn__6824.invoke(core.clj:6126)
at clojure.core$load.invokeStatic(core.clj:6125)
at clojure.core$load.doInvoke(core.clj:6109)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.lang.Var.invoke(Var.java:384)
at clojure.lang.Util.loadWithClass(Util.java:250)
at bcbio.variation.recall.main.(Unknown Source)
Caused by: java.io.IOException: Transport endpoint is not connected
at java.io.UnixFileSystem.canonicalize0(Native Method)
at java.io.UnixFileSystem.canonicalize(UnixFileSystem.java:172)
at java.io.File.getCanonicalPath(File.java:618)
at java.io.File.getCanonicalFile(File.java:643)
at me.raynes.fs__init.load(Unknown Source)
at me.raynes.fs__init.(Unknown Source)
... 98 more

At the end I attach my installed conda packages in the active env.
Do you have any idea what causes this error and could you please help me fix it?

Thank you!

This is my miniconda3 env:
Name Version Build Channel
_libgcc_mutex 0.1 main
alabaster 0.7.12 py27_0
anaconda 2019.10 py27_0
anaconda-client 1.7.2 py27_0
anaconda-project 0.8.3 py_0
argcomplete 1.12.1 py_0
argh 0.26.1 py27_0 bioconda
arrow 0.13.1 py27_0
asn1crypto 1.0.1 py27_0
astroid 1.6.5 py27_0
astropy 2.0.9 py27hdd07704_0
atomicwrites 1.3.0 py27_1
attrs 19.2.0 py_0
babel 2.7.0 py_0
backports 1.0 py_2
backports.functools_lru_cache 1.5 py_2
backports.os 0.1.1 py27_0
backports.shutil_get_terminal_size 1.0.0 py27_2
backports_abc 0.5 py27_0
bcbio-nextgen 1.1.6a py27_0 bioconda
bcbio-variation-recall 0.2.6 0 bioconda
bcftools 1.9 ha228f0b_4 bioconda
beautifulsoup4 4.8.0 py27_0
bedtools 2.29.2 hc088bd4_0 bioconda
bioblend 0.12.0 py_0 bioconda
biopython 1.68 py27_0 bioconda
bitarray 1.0.1 py27h7b6447c_0
bkcharts 0.2 py27_0
blas 1.0 mkl
bleach 3.1.0 py27_0
blosc 1.16.3 hd408876_0
bokeh 1.3.4 py27_0
boto 2.49.0 py27_0
bottleneck 1.2.1 py27h035aef0_1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2019.8.28 0
cairo 1.14.12 h8948797_3
cdecimal 2.3 py27h14c3975_3
certifi 2019.9.11 py27_0
cffi 1.12.3 py27h2e261b9_0
chardet 3.0.4 py27_1003
click 7.0 py27_0
cloudpickle 1.2.2 py_0
clyent 1.2.2 py27_1
colorama 0.4.1 py27_0
coloredlogs 10.0 py27_0
conda 4.8.2 py27_0 conda-forge
conda-package-handling 1.6.0 py27h516909a_1 conda-forge
configparser 4.0.2 py27_0
contextlib2 0.6.0 py_0
coverage 5.0 py27h7b6447c_0
cryptography 2.7 py27h1ba5d50_0
curl 7.65.3 hbc83047_0
cycler 0.10.0 py27_0
cython 0.29.13 py27he6710b0_0
cytoolz 0.10.0 py27h7b6447c_0
cyvcf2 0.11.6 py27hce88a48_0 bioconda
dask 1.2.2 py_0
dask-core 1.2.2 py_0
dbus 1.13.6 h746ee38_0
decorator 4.4.0 py27_1
defusedxml 0.6.0 py_0
distributed 1.28.1 py27_0
dnapi 1.1 pyh864c0ab_4 bioconda
docutils 0.15.2 py27_0
entrypoints 0.3 py27_0
enum34 1.1.6 py27_1
et_xmlfile 1.0.1 py27_0
expat 2.2.6 he6710b0_0
fadapa 0.3.1 pyh864c0ab_2 bioconda
fastcache 1.1.0 py27h7b6447c_0
filelock 3.0.12 py_0
flask 1.1.1 py_0
fontconfig 2.13.0 h9420a91_0
freebayes 0.9.21.7 0 bioconda
freetype 2.9.1 h8a8886c_1
fribidi 1.0.5 h7b6447c_0
funcsigs 1.0.2 py27_0
functools32 3.2.3.2 py27_1
future 0.17.1 py27_0
futures 3.3.0 py27_0
gatk-framework 3.6.24 5 bioconda
geneimpacts 0.3.7 pyh864c0ab_2 bioconda
get_terminal_size 1.0.0 haa9412d_0
gevent 1.4.0 py27h7b6447c_0
gffutils 0.9 py_1 bioconda
glib 2.56.2 hd408876_0
glob2 0.7 py_0
gmp 6.1.2 h6c8ec71_1
gmpy2 2.0.8 py27h10f8cd9_2
graphite2 1.3.13 h23475e2_0
greenlet 0.4.15 py27h7b6447c_0
grin 1.2.1 py27_4
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.9.0 py27h7918eee_0
harfbuzz 1.8.8 hffaf4a1_0
hdf5 1.10.4 hb1b8bf9_0
heapdict 1.0.1 py_0
html5lib 1.0.1 py27_0
htslib 1.9 ha228f0b_7 bioconda
humanfriendly 4.18 py27_0
icu 58.2 h9c2bf20_1
idna 2.8 py27_0
imageio 2.6.0 py27_0
imagesize 1.1.0 py27_0
importlib_metadata 0.23 py27_0
intel-openmp 2019.4 243
ipaddress 1.0.22 py27_0
ipykernel 4.10.0 py27_0
ipyparallel 6.2.4 py27_0
ipython 5.8.0 py27_0
ipython-cluster-helper 0.6.4 pyh864c0ab_1 bioconda
ipython_genutils 0.2.0 py27_0
ipywidgets 7.5.1 py_0
isort 4.3.21 py27_0
itsdangerous 1.1.0 py27_0
jbig 2.1 hdba287a_0
jdcal 1.4.1 py_0
jedi 0.15.1 py27_0
jinja2 2.10.3 py_0
joblib 0.14.1 py_0
jpeg 9b h024ee3a_2
jsonschema 3.0.2 py27_0
jupyter 1.0.0 py27_7
jupyter_client 5.3.3 py27_1
jupyter_console 5.2.0 py27_1
jupyter_core 4.5.0 py_0
jupyterlab 0.33.11 py27_0
jupyterlab_launcher 0.11.2 py27h28b3542_0
kiwisolver 1.1.0 py27he6710b0_0
krb5 1.16.1 h173b8e3_7
lazy-object-proxy 1.4.2 py27h7b6447c_0
libarchive 3.3.3 h5d8350f_5
libcurl 7.65.3 h20c2e04_0
libdeflate 1.0 h14c3975_1 bioconda
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
liblief 0.9.0 h7725739_2
libpng 1.6.37 hbc83047_0
libsodium 1.0.16 h1bed415_0
libsolv 0.7.16 h8b12597_0 conda-forge
libssh2 1.8.2 h1ba5d50_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.0.10 h2733197_2
libtool 2.4.6 h7b6447c_5
libuuid 1.0.3 h1bed415_2
libxcb 1.13 h1bed415_1
libxml2 2.9.9 hea5a465_1
libxslt 1.1.33 h7d1a2b0_0
linecache2 1.0.0 py27_0
llvmlite 0.29.0 py27hd408876_0
locket 0.2.0 py27_1
logbook 1.4.3 py27h14c3975_0 bioconda
lxml 4.4.1 py27hefd8a0e_0
lz4-c 1.8.1.2 h14c3975_0
lzo 2.10 h49e0be7_2
mamba 0.1.0 py27hc9558a2_2 conda-forge
markupsafe 1.1.1 py27h7b6447c_0
matplotlib 2.2.3 py27hb69df0a_0
mccabe 0.6.1 py27_1
mirtop 0.4.23 pyh864c0ab_1 bioconda
mistune 0.8.4 py27h7b6447c_0
mkl 2019.4 243
mkl-service 2.3.0 py27he904b0f_0
mkl_fft 1.0.14 py27ha843d7b_0
mkl_random 1.1.0 py27hd6b4f25_0
mmtf-python 1.0.2 py27_0 bioconda
mock 3.0.5 py27_0
more-itertools 5.0.0 py27_0
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.1 hdf1c602_3
mpmath 1.1.0 py27_0
msgpack-python 0.6.1 py27hfd86e86_1
multipledispatch 0.6.0 py27_0
nbconvert 5.6.0 py27_1
nbformat 4.4.0 py27_0
ncurses 6.1 he6710b0_1
netifaces 0.10.4 py27_1 bioconda
networkx 2.2 py27_1
nltk 3.4.5 py27_0
nose 1.3.7 py27_2
notebook 5.7.8 py27_0
numba 0.45.1 py27h962f231_0
numexpr 2.7.0 py27h9e4a6bb_0
numpy 1.16.5 py27h7e9f1db_0
numpy-base 1.16.5 py27hde5b4d6_0
numpydoc 0.9.1 py_0
olefile 0.46 py27_0
openjdk 8.0.152 h7b6447c_3
openpyxl 2.6.3 py_0
openssl 1.1.1d h7b6447c_2
packaging 19.2 py_0
pandas 0.24.2 py27he6710b0_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py27_1
pango 1.42.4 h049681c_0
parso 0.5.1 py_0
partd 1.0.0 py_0
patchelf 0.9 he6710b0_3
path.py 11.5.0 py27_0
pathlib2 2.3.5 py27_0
patsy 0.5.1 py27_0
pcre 8.43 he6710b0_0
pep8 1.7.1 py27_0
pexpect 4.7.0 py27_0
pickleshare 0.7.5 py27_0
pillow 6.2.0 py27h34e0f95_0
pip 19.2.3 py27_0
pixman 0.38.0 h7b6447c_0
pkginfo 1.5.0.1 py27_0
platypus-variant 0.8.1.2 py27hb763d49_0 bioconda
pluggy 0.13.0 py27_0
ply 3.11 py27_0
progressbar2 3.37.1 py27_0
prometheus_client 0.7.1 py_0
prompt_toolkit 1.0.15 py27_0
psutil 5.6.3 py27h7b6447c_0
ptyprocess 0.6.0 py27_0
py 1.8.0 py27_0
py-lief 0.9.0 py27h7725739_2
pybedtools 0.8.1 py27he513fc3_0 bioconda
pycairo 1.18.1 py27h2a1e443_0
pycodestyle 2.5.0 py27_0
pycosat 0.6.3 py27h14c3975_0
pycparser 2.19 py27_0
pycrypto 2.6.1 py27h14c3975_9
pycurl 7.43.0.3 py27h1ba5d50_0
pyfaidx 0.5.9.1 pyh864c0ab_1 bioconda
pyflakes 2.1.1 py27_0
pygments 2.4.2 py_0
pylint 1.9.2 py27_0
pyodbc 4.0.27 py27he6710b0_0
pyopenssl 19.0.0 py27_0
pyparsing 2.4.2 py_0
pyqt 5.9.2 py27h05f1152_2
pyrsistent 0.15.4 py27h7b6447c_0
pysam 0.15.3 py27hda2845c_1 bioconda
pysocks 1.7.1 py27_0
pytables 3.5.2 py27h71ec239_1
pytest 4.6.2 py27_0
pytest-cov 2.10.1 py_0
pytest-mock 2.0.0 py_0
pytest-runner 5.2 py_0
python 2.7.16 h9bab390_7
python-dateutil 2.8.0 py27_0
python-libarchive-c 2.8 py27_13
python-utils 2.3.0 py27_0
pytz 2019.3 py_0
pyvcf 0.6.8 py27_0 bioconda
pywavelets 1.0.3 py27hdd07704_1
pyyaml 5.1.2 py27h7b6447c_0
pyzmq 18.1.0 py27he6710b0_0
qt 5.9.7 h5867ecd_1
qtawesome 0.6.0 py_0
qtconsole 4.5.5 py_0
qtpy 1.9.0 py_0
readline 7.0 h7b6447c_5
reportlab 3.5.26 py27he686d34_0
requests 2.22.0 py27_0
requests-toolbelt 0.5.0 py27_0 bioconda
ripgrep 0.10.0 hc07d326_0
rope 0.14.0 py_0
ruamel_yaml 0.15.46 py27h14c3975_0
sambamba 0.6.6 2 bioconda
samtools 1.9 h10a08f8_12 bioconda
scandir 1.10.0 py27h7b6447c_0
scikit-image 0.14.2 py27he6710b0_0
scikit-learn 0.20.3 py27hd81dba3_0
scipy 1.2.1 py27h7c811a0_0
seaborn 0.9.0 py27_0
send2trash 1.5.0 py27_0
seqcluster 1.2.7 pyh864c0ab_1 bioconda
setuptools 41.4.0 py27_0
simplegeneric 0.8.1 py27_2
simplejson 3.8.1 py27_0 bioconda
singledispatch 3.4.0.3 py27_0
sip 4.19.8 py27hf484d3e_0
six 1.12.0 py27_0
snappy 1.1.7 hbae5bb6_3
snowballstemmer 2.0.0 py_0
sortedcollections 1.1.2 py27_0
sortedcontainers 2.1.0 py27_0
soupsieve 1.9.3 py27_0
sphinx 1.8.5 py27_0
sphinxcontrib 1.0 py27_1
sphinxcontrib-websupport 1.1.2 py_0
spyder 3.3.6 py27_0
spyder-kernels 0.5.2 py27_0
sqlalchemy 1.3.9 py27h7b6447c_0
sqlite 3.30.0 h7b6447c_0
ssl_match_hostname 3.7.0.1 py27_0
statsmodels 0.10.1 py27hdd07704_0
subprocess32 3.5.4 py27h7b6447c_0
sympy 1.4 py27_0
tabulate 0.8.3 py27_0
tbb 2019.4 hfd86e86_0
tblib 1.4.0 py_0
terminado 0.8.2 py27_0
testpath 0.4.2 py27_0
tk 8.6.8 hbc83047_0
toolz 0.10.0 py_0
tornado 5.1.1 py27h7b6447c_0
tqdm 4.36.1 py_0
traceback2 1.4.0 py27_0
traitlets 4.3.3 py27_0
typing 3.7.4.1 py27_0
unicodecsv 0.14.1 py27_0
unittest2 1.1.0 py27_0
unixodbc 2.3.7 h14c3975_0
urllib3 1.24.2 py27_0
vcflib 1.0.0_rc2 h56106d0_2 bioconda
viennarna 2.4.14 py27h8b12597_0 bioconda
vt 2015.11.10 he941832_3 bioconda
wcwidth 0.1.7 py27_0
webencodings 0.5.1 py27_1
werkzeug 0.16.0 py_0
wheel 0.33.6 py27_0
widgetsnbextension 3.5.1 py27_0
wrapt 1.11.2 py27h7b6447c_0
wurlitzer 1.0.3 py27_0
xlrd 1.2.0 py27_0
xlsxwriter 1.2.1 py_0
xlwt 1.3.0 py27_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
yamllint 1.2.1 py27_0 bioconda
zeromq 4.3.1 he6710b0_3
zict 1.0.0 py_0
zipp 0.6.0 py_0
zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0
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