Xiaofei-git
commented
2 years ago In fact, it is paired-end. I do't know why it is considered as single-end "2021-07-08 14:00:37,753 The input dataset is considered as a single-end dataset".
Closed Xiaofei-git closed 2 years ago
Xiaofei-git
commented
2 years ago In fact, it is paired-end. I do't know why it is considered as single-end "2021-07-08 14:00:37,753 The input dataset is considered as a single-end dataset".
hyunhwan-jeong
commented
2 years ago Hi @Xiaofei-git, the first thing I could figure out is that the file name has to be example/CTRL_1_R1.fastq example/CTRL_1_R2.fastq instead of example/CTRL_1_R1.fastq example/CTRL_2_R1.fastq. CTRL_1_R1.fastq and CTRL_2_R1.fastq are from different samples, so SalmonTE would not consider them as paired-end samples.
Regarding another error, I may need to have more inputs from you. Could you inform me what you see either pip list or conda list?
Thank you,
Hyun-Hwan Jeong
Xiaofei-git
commented
2 years ago Hi @Xiaofei-git, the first thing I could figure out is that the file name has to be
example/CTRL_1_R1.fastq example/CTRL_1_R2.fastqinstead ofexample/CTRL_1_R1.fastq example/CTRL_2_R1.fastq.CTRL_1_R1.fastqandCTRL_2_R1.fastqare from different samples, so SalmonTE would not consider them as paired-end samples.Regarding another error, I may need to have more inputs from you. Could you inform me what you see either
pip listorconda list?Thank you,
Hyun-Hwan Jeong
Yes, you are right. I did't realize I used different samples of R1.
For another error, here are the what I see from "pip list" and "conda list":
$ pip list
Package Version
---------------------------------- -----------------
alabaster 0.7.12
amply 0.1.4
anaconda-client 1.7.2
anaconda-navigator 1.10.0
anaconda-project 0.8.3
appdirs 1.4.4
applaunchservices 0.2.1
appnope 0.1.0
appscript 1.1.1
argh 0.26.2
argon2-cffi 20.1.0
asn1crypto 1.4.0
astroid 2.4.2
astropy 4.0.2
async-generator 1.10
atomicwrites 1.4.0
attrs 21.2.0
autopep8 1.5.4
Babel 2.8.1
backcall 0.2.0
backports.functools-lru-cache 1.6.1
backports.shutil-get-terminal-size 1.0.0
backports.tempfile 1.0
backports.weakref 1.0.post1
beautifulsoup4 4.9.3
biopython 1.78
bitarray 1.6.1
bkcharts 0.2
bleach 3.2.1
bokeh 2.2.3
boto 2.49.0
boto3 1.17.106
botocore 1.20.106
Bottleneck 1.3.2
brotlipy 0.7.0
bs4 0.0.1
certifi 2021.5.30
cffi 1.14.3
chardet 4.0.0
click 7.1.2
cloudpickle 1.6.0
clyent 1.2.2
colorama 0.4.4
conda 4.10.1
conda-build 3.20.5
conda-package-handling 1.7.2
conda-verify 3.4.2
ConfigArgParse 1.5.1
connection-pool 0.0.3
contextlib2 0.6.0.post1
cryptography 3.1.1
cycler 0.10.0
Cython 0.29.21
cytoolz 0.11.0
dask 2.30.0
datrie 0.8.2
decorator 4.4.2
defusedxml 0.6.0
diff-match-patch 20200713
distributed 2.30.1
docopt 0.6.2
docutils 0.17.1
entrypoints 0.3
et-xmlfile 1.0.1
fastcache 1.1.0
filelock 3.0.12
flake8 3.8.4
Flask 1.1.2
fsspec 0.8.3
future 0.18.2
gevent 20.9.0
gitdb 4.0.7
GitPython 3.1.18
glob2 0.7
gmpy2 2.0.8
greenlet 0.4.17
gseapy 0.9.5
h5py 2.10.0
HeapDict 1.0.1
html5lib 1.1
idna 2.10
imageio 2.9.0
imagesize 1.2.0
importlib-metadata 2.0.0
iniconfig 1.1.1
intervaltree 3.1.0
ipykernel 5.3.4
ipython 7.19.0
ipython-genutils 0.2.0
ipywidgets 7.5.1
isort 5.6.4
itsdangerous 1.1.0
jdcal 1.4.1
jedi 0.17.1
Jinja2 3.0.1
jmespath 0.10.0
joblib 0.17.0
json5 0.9.5
jsonschema 3.2.0
jupyter 1.0.0
jupyter-client 6.1.7
jupyter-console 6.2.0
jupyter-core 4.6.3
jupyterlab 2.2.6
jupyterlab-pygments 0.1.2
jupyterlab-server 1.2.0
keyring 21.4.0
kiwisolver 1.3.0
lazy-object-proxy 1.4.3
libarchive-c 2.9
llvmlite 0.34.0
locket 0.2.0
lxml 4.6.1
MarkupSafe 2.0.1
matplotlib 3.3.2
mccabe 0.6.1
mistune 0.8.4
mkl-fft 1.2.0
mkl-random 1.1.1
mkl-service 2.3.0
mock 4.0.2
more-itertools 8.6.0
mpmath 1.1.0
msgpack 1.0.0
multipledispatch 0.6.0
navigator-updater 0.2.1
nbclient 0.5.1
nbconvert 6.0.7
nbformat 5.0.8
nest-asyncio 1.4.2
networkx 2.5.1
nltk 3.5
nose 1.3.7
notebook 6.1.4
numba 0.51.2
numexpr 2.7.1
numpy 1.19.2
numpydoc 1.1.0
olefile 0.46
openpyxl 3.0.5
packaging 20.4
pandas 1.1.3
pandocfilters 1.4.3
parso 0.7.0
partd 1.1.0
path 15.0.0
pathlib2 2.3.5
pathtools 0.1.2
patsy 0.5.1
pep8 1.7.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 8.0.1
pip 20.2.4
pkginfo 1.6.1
pluggy 0.13.1
ply 3.11
prometheus-client 0.8.0
prompt-toolkit 3.0.8
psutil 5.7.2
ptyprocess 0.6.0
PuLP 2.4
py 1.9.0
pycodestyle 2.6.0
pycosat 0.6.3
pycparser 2.20
pycurl 7.43.0.6
pydocstyle 5.1.1
pyflakes 2.2.0
Pygments 2.7.2
pylint 2.6.0
pyodbc 4.0.0-unsupported
pyOpenSSL 19.1.0
pyparsing 2.4.7
pyrsistent 0.18.0
PySocks 1.7.1
pytest 0.0.0
python-dateutil 2.8.1
python-jsonrpc-server 0.4.0
python-language-server 0.35.1
pytz 2020.1
PyWavelets 1.1.1
PyYAML 5.4.1
pyzmq 19.0.2
QDarkStyle 2.8.1
QtAwesome 1.0.1
qtconsole 4.7.7
QtPy 1.9.0
ratelimiter 1.2.0.post0
regex 2020.10.15
requests 2.25.1
rope 0.18.0
Rtree 0.9.4
ruamel-yaml 0.15.87
s3transfer 0.4.2
scikit-image 0.17.2
scikit-learn 0.23.2
scipy 1.5.2
seaborn 0.11.0
Send2Trash 1.5.0
setuptools 57.1.0
simplegeneric 0.8.1
singledispatch 3.4.0.3
six 1.16.0
smart-open 5.1.0
smmap 4.0.0
snakemake 5.1.5
snowballstemmer 2.0.0
sortedcollections 1.2.1
sortedcontainers 2.2.2
soupsieve 2.0.1
Sphinx 3.2.1
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 1.0.3
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.4
sphinxcontrib-websupport 1.2.4
spyder 4.1.5
spyder-kernels 1.9.4
SQLAlchemy 1.3.20
statsmodels 0.12.0
stopit 1.1.2
sympy 1.6.2
tables 3.6.1
tabulate 0.8.9
tblib 1.7.0
terminado 0.9.1
testpath 0.4.4
threadpoolctl 2.1.0
tifffile 2020.10.1
toml 0.10.1
toolz 0.11.1
toposort 1.6
tornado 6.0.4
tqdm 4.50.2
traitlets 5.0.5
typing-extensions 3.7.4.3
ujson 4.0.1
unicodecsv 0.14.1
urllib3 1.26.6
watchdog 0.10.3
wcwidth 0.2.5
webencodings 0.5.1
Werkzeug 1.0.1
wheel 0.35.1
widgetsnbextension 3.5.1
wrapt 1.12.1
wurlitzer 2.0.1
xlrd 1.2.0
XlsxWriter 1.3.7
xlwings 0.20.8
xlwt 1.3.0
xmltodict 0.12.0
yapf 0.30.0
zict 2.0.0
zipp 3.4.0
zope.event 4.5.0
zope.interface 5.1.2$ conda list
# packages in environment at /Users/xwang/anaconda3:
#
# Name Version Build Channel
_ipyw_jlab_nb_ext_conf 0.1.0 py38_0
alabaster 0.7.12 py_0
anaconda 2020.11 py38_0
anaconda-client 1.7.2 py38_0
anaconda-navigator 1.10.0 py38_0
anaconda-project 0.8.4 py_0
appdirs 1.4.4 pypi_0 pypi
applaunchservices 0.2.1 py_0
appnope 0.1.0 py38_1001
appscript 1.1.1 py38haf1e3a3_0
argh 0.26.2 py38_0
argon2-cffi 20.1.0 py38haf1e3a3_1
asn1crypto 1.4.0 py_0
astroid 2.4.2 py38_0
astropy 4.0.2 py38haf1e3a3_0
async_generator 1.10 py_0
atomicwrites 1.4.0 py_0
attrs 21.2.0 pypi_0 pypi
autopep8 1.5.4 py_0
babel 2.8.1 pyhd3eb1b0_0
backcall 0.2.0 py_0
backports 1.0 py_2
backports.functools_lru_cache 1.6.1 py_0
backports.shutil_get_terminal_size 1.0.0 py38_2
backports.tempfile 1.0 py_1
backports.weakref 1.0.post1 py_1
beautifulsoup4 4.9.3 pyhb0f4dca_0
bedtools 2.30.0 h6eb76b4_0 bioconda
bioawk 1.0 h2573ce8_5 bioconda
biopython 1.78 py38h96a0964_2 conda-forge
bitarray 1.6.1 py38h9ed2024_0
bkcharts 0.2 py38_0
blas 1.0 mkl
bleach 3.2.1 py_0
blosc 1.20.1 hab81aa3_0
bokeh 2.2.3 py38_0
boto 2.49.0 py38_0
boto3 1.17.106 pypi_0 pypi
botocore 1.20.106 pypi_0 pypi
bottleneck 1.3.2 py38hf1fa96c_1
brotlipy 0.7.0 py38haf1e3a3_1000
bs4 0.0.1 pypi_0 pypi
bzip2 1.0.8 h1de35cc_0
ca-certificates 2020.10.14 0
certifi 2021.5.30 pypi_0 pypi
cffi 1.14.3 py38hed5b41f_0
chardet 4.0.0 pypi_0 pypi
click 7.1.2 py_0
cloudpickle 1.6.0 py_0
clyent 1.2.2 py38_1
colorama 0.4.4 py_0
conda 4.10.1 py38hecd8cb5_1
conda-build 3.20.5 py38_1
conda-env 2.6.0 1
conda-package-handling 1.7.2 py38h22f3db7_0
conda-verify 3.4.2 py_1
configargparse 1.5.1 pypi_0 pypi
contextlib2 0.6.0.post1 py_0
cryptography 3.1.1 py38hddc9c9b_0
curl 7.71.1 hb0a8c7a_1
cycler 0.10.0 py38_0
cython 0.29.21 py38hb1e8313_0
cytoolz 0.11.0 py38haf1e3a3_0
dask 2.30.0 py_0
dask-core 2.30.0 py_0
datrie 0.8.2 pypi_0 pypi
dbus 1.13.18 h18a8e69_0
decorator 4.4.2 py_0
defusedxml 0.6.0 py_0
diff-match-patch 20200713 py_0
distributed 2.30.1 py38hecd8cb5_0
docutils 0.17.1 pypi_0 pypi
entrypoints 0.3 py38_0
et_xmlfile 1.0.1 py_1001
expat 2.2.10 hb1e8313_2
fastcache 1.1.0 py38h1de35cc_0
filelock 3.0.12 py_0
flake8 3.8.4 py_0
flask 1.1.2 py_0
freetype 2.10.4 ha233b18_0
fsspec 0.8.3 py_0
future 0.18.2 py38_1
get_terminal_size 1.0.0 h7520d66_0
gettext 0.19.8.1 hb0f4f8b_2
gevent 20.9.0 py38haf1e3a3_0
glib 2.66.1 h9bbe63b_0
glob2 0.7 py_0
gmp 6.1.2 hb37e062_1
gmpy2 2.0.8 py38h6ef4df4_3
greenlet 0.4.17 py38haf1e3a3_0
gseapy 0.9.5 py_1 bioconda
h5py 2.10.0 py38h3134771_0
hdf5 1.10.4 hfa1e0ec_0
heapdict 1.0.1 py_0
html5lib 1.1 py_0
icu 58.2 h0a44026_3
idna 2.10 py_0
imageio 2.9.0 py_0
imagesize 1.2.0 py_0
importlib-metadata 2.0.0 py_1
importlib_metadata 2.0.0 1
iniconfig 1.1.1 py_0
intel-openmp 2019.4 233
intervaltree 3.1.0 py_0
ipykernel 5.3.4 py38h5ca1d4c_0
ipython 7.19.0 py38h01d92e1_0
ipython_genutils 0.2.0 py38_0
ipywidgets 7.5.1 py_1
isort 5.6.4 py_0
itsdangerous 1.1.0 py_0
jbig 2.1 h4d881f8_0
jdcal 1.4.1 py_0
jedi 0.17.1 py38_0
jinja2 3.0.1 pypi_0 pypi
jmespath 0.10.0 pypi_0 pypi
joblib 0.17.0 py_0
jpeg 9b he5867d9_2
json5 0.9.5 py_0
jsonschema 3.2.0 py_2
jupyter 1.0.0 py38_7
jupyter_client 6.1.7 py_0
jupyter_console 6.2.0 py_0
jupyter_core 4.6.3 py38_0
jupyterlab 2.2.6 py_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 1.2.0 py_0
keyring 21.4.0 py38_1
kiwisolver 1.3.0 py38h23ab428_0
krb5 1.18.2 h75d18d8_0
lazy-object-proxy 1.4.3 py38h1de35cc_0
lcms2 2.11 h92f6f08_0
libarchive 3.4.2 haa3ed63_0
libcurl 7.71.1 h8a08a2b_1
libcxx 10.0.0 1
libedit 3.1.20191231 h1de35cc_1
libffi 3.3 hb1e8313_2
libgcc 4.8.5 hdbeacc1_10
libgfortran 3.0.1 h93005f0_2
libiconv 1.16 h1de35cc_0
liblief 0.10.1 h0a44026_0
libllvm10 10.0.1 h76017ad_5
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 h1de35cc_0
libspatialindex 1.9.3 h0a44026_0
libssh2 1.9.0 ha12b0ac_1
libtiff 4.1.0 hcb84e12_1
libxml2 2.9.10 h7cdb67c_3
libxslt 1.1.34 h83b36ba_0
llvm-openmp 10.0.0 h28b9765_0
llvmlite 0.34.0 py38h739e7dc_4
locket 0.2.0 py38_1
lxml 4.6.1 py38h63b7cb6_0
lz4-c 1.9.2 h79c402e_3
lzo 2.10 haf1e3a3_2
markupsafe 2.0.1 pypi_0 pypi
matplotlib 3.3.2 0
matplotlib-base 3.3.2 py38h181983e_0
mccabe 0.6.1 py38_1
mistune 0.8.4 py38h1de35cc_1001
mkl 2019.4 233
mkl-service 2.3.0 py38hfbe908c_0
mkl_fft 1.2.0 py38hc64f4ea_0
mkl_random 1.1.1 py38h959d312_0
mock 4.0.2 py_0
more-itertools 8.6.0 pyhd3eb1b0_0
mpc 1.1.0 h6ef4df4_1
mpfr 4.0.2 h9066e36_1
mpmath 1.1.0 py38_0
msgpack-python 1.0.0 py38h04f5b5a_1
multipledispatch 0.6.0 py38_0
navigator-updater 0.2.1 py38_0
nbclient 0.5.1 py_0
nbconvert 6.0.7 py38_0
nbformat 5.0.8 py_0
ncurses 6.2 h0a44026_1
nest-asyncio 1.4.2 pyhd3eb1b0_0
networkx 2.5.1 pypi_0 pypi
nltk 3.5 py_0
nose 1.3.7 py38_1004
notebook 6.1.4 py38_0
numba 0.51.2 py38h6440ff4_1
numexpr 2.7.1 py38hce01a72_0
numpy 1.19.2 py38h456fd55_0
numpy-base 1.19.2 py38hcfb5961_0
numpydoc 1.1.0 pyhd3eb1b0_1
olefile 0.46 py_0
openjdk 11.0.6 h7bc2e8c_1
openpyxl 3.0.5 py_0
openssl 1.1.1h haf1e3a3_0
packaging 20.4 py_0
pandas 1.1.3 py38hb1e8313_0
pandoc 2.11 h0dc7051_0
pandocfilters 1.4.3 py38hecd8cb5_1
parso 0.7.0 py_0
partd 1.1.0 py_0
path 15.0.0 py38_0
path.py 12.5.0 0
pathlib2 2.3.5 py38_1
pathtools 0.1.2 py_1
patsy 0.5.1 py38_0
pcre 8.44 hb1e8313_0
pep8 1.7.1 py38_0
perl 5.26.2 h4e221da_0
perl-bioperl 1.6.924 4 bioconda/label/cf201901
perl-threaded 5.26.0 0 bioconda
perl-yaml 1.29 pl526_0 bioconda
pexpect 4.8.0 py38_1
pickleshare 0.7.5 py38_1001
pillow 8.0.1 py38h5270095_0
pip 20.2.4 py38hecd8cb5_0
pkginfo 1.6.1 py38hecd8cb5_0
pluggy 0.13.1 py38_0
ply 3.11 py38_0
prometheus_client 0.8.0 py_0
prompt-toolkit 3.0.8 py_0
prompt_toolkit 3.0.8 0
psutil 5.7.2 py38haf1e3a3_0
ptyprocess 0.6.0 py38_0
py 1.9.0 py_0
py-lief 0.10.1 py38haf313ee_0
pycodestyle 2.6.0 py_0
pycosat 0.6.3 py38h1de35cc_1
pycparser 2.20 py_2
pycurl 7.43.0.6 py38hddc9c9b_0
pydocstyle 5.1.1 py_0
pyflakes 2.2.0 py_0
pygments 2.7.2 pyhd3eb1b0_0
pylint 2.6.0 py38_0
pyodbc 4.0.30 py38h0a44026_0
pyopenssl 19.1.0 py_1
pyparsing 2.4.7 py_0
pyqt 5.9.2 py38h655552a_2
pyrsistent 0.18.0 pypi_0 pypi
pysocks 1.7.1 py38_1
pytables 3.6.1 py38h4727e94_0
pytest 6.1.1 py38_0
python 3.8.5 h26836e1_1
python-dateutil 2.8.1 py_0
python-jsonrpc-server 0.4.0 py_0
python-language-server 0.35.1 py_0
python-libarchive-c 2.9 py_0
python.app 2 py38_10
python_abi 3.8 1_cp38 conda-forge
pytz 2020.1 py_0
pywavelets 1.1.1 py38haf1e3a3_2
pyyaml 5.4.1 pypi_0 pypi
pyzmq 19.0.2 py38hb1e8313_1
qdarkstyle 2.8.1 py_0
qt 5.9.7 h468cd18_1
qtawesome 1.0.1 py_0
qtconsole 4.7.7 py_0
qtpy 1.9.0 py_0
ratelimiter 1.2.0.post0 pypi_0 pypi
readline 8.0 h1de35cc_0
regex 2020.10.15 py38haf1e3a3_0
requests 2.25.1 pypi_0 pypi
ripgrep 12.1.1 0
rope 0.18.0 py_0
rtree 0.9.4 py38_1
ruamel_yaml 0.15.87 py38haf1e3a3_1
s3transfer 0.4.2 pypi_0 pypi
scikit-image 0.17.2 py38h81aa140_0
scikit-learn 0.23.2 py38h959d312_0
scipy 1.5.2 py38h2515648_0
seaborn 0.11.0 py_0
send2trash 1.5.0 py38_0
setuptools 57.1.0 pypi_0 pypi
simplegeneric 0.8.1 py38_2
singledispatch 3.4.0.3 py_1001
sip 4.19.8 py38h0a44026_0
six 1.16.0 pypi_0 pypi
snakemake 5.1.5 pypi_0 pypi
snowballstemmer 2.0.0 py_0
snpeff 5.0 0 bioconda
snpsift 4.3.1t 2 bioconda
sortedcollections 1.2.1 py_0
sortedcontainers 2.2.2 py_0
soupsieve 2.0.1 py_0
sphinx 3.2.1 py_0
sphinxcontrib 1.0 py38_1
sphinxcontrib-applehelp 1.0.2 py_0
sphinxcontrib-devhelp 1.0.2 py_0
sphinxcontrib-htmlhelp 1.0.3 py_0
sphinxcontrib-jsmath 1.0.1 py_0
sphinxcontrib-qthelp 1.0.3 py_0
sphinxcontrib-serializinghtml 1.1.4 py_0
sphinxcontrib-websupport 1.2.4 py_0
spyder 4.1.5 py38_0
spyder-kernels 1.9.4 py38_0
sqlalchemy 1.3.20 py38h9ed2024_0
sqlite 3.33.0 hffcf06c_0
statsmodels 0.12.0 py38haf1e3a3_0
sympy 1.6.2 py38hecd8cb5_1
tblib 1.7.0 py_0
terminado 0.9.1 py38_0
testpath 0.4.4 py_0
threadpoolctl 2.1.0 pyh5ca1d4c_0
tifffile 2020.10.1 py38h0cf3a3e_2
tk 8.6.10 hb0a8c7a_0
toml 0.10.1 py_0
toolz 0.11.1 py_0
tornado 6.0.4 py38h1de35cc_1
tqdm 4.50.2 py_0
traitlets 5.0.5 py_0
typing_extensions 3.7.4.3 py_0
ujson 4.0.1 py38hb1e8313_0
unicodecsv 0.14.1 py38_0
unixodbc 2.3.9 haf1e3a3_0
urllib3 1.26.6 pypi_0 pypi
watchdog 0.10.3 py38haf1e3a3_0
wcwidth 0.2.5 py_0
webencodings 0.5.1 py38_1
werkzeug 1.0.1 py_0
wheel 0.35.1 py_0
widgetsnbextension 3.5.1 py38_0
wrapt 1.12.1 pypi_0 pypi
wurlitzer 2.0.1 py38_0
xlrd 1.2.0 py_0
xlsxwriter 1.3.7 py_0
xlwings 0.20.8 py38_0
xlwt 1.3.0 py38_0
xmltodict 0.12.0 py_0
xz 5.2.5 h1de35cc_0
yaml 0.2.5 haf1e3a3_0
yapf 0.30.0 py_0
zeromq 4.3.3 hb1e8313_3
zict 2.0.0 py_0
zipp 3.4.0 pyhd3eb1b0_0
zlib 1.2.11 h1de35cc_3
zope 1.0 py38_1
zope.event 4.5.0 py38_0
zope.interface 5.1.2 py38haf1e3a3_0
zstd 1.4.5 h41d2c2f_0Dear @hyunhwan-jeong ,
I am checking back to see do you have any idea about the error?
Thanks a lot!
BEST,
Xiaofei
hyunhwan-jeong
commented
2 years ago Hi @Xiaofei-git,
I guess the snakemake version has a compatibility issue with SalmonTE. I believe it could be solved if you install the latest version of snakemake. You can install the latest version with the following command - pip install snakemake --upgrade
Hyun-Hwan Jeong
Xiaofei-git
commented
2 years ago @hyunhwan-jeong
The error was fixed with latest version of snakelike.
$ snakemake -v 6.6.1
But, got another error as below
$ SalmonTE.py quant --reference=hs example
2021-07-20 07:45:00,108 Starting quantification mode
2021-07-20 07:45:00,108 Collecting FASTQ files...
2021-07-20 07:45:00,108 SalmonTE assumes that 'example' is a directory, and SalmonTE will search any FASTQ file in the directory.
2021-07-20 07:45:00,115 The input dataset is considered as a paired-ends dataset.
2021-07-20 07:45:00,115 Collected 4 FASTQ files.
2021-07-20 07:45:00,115 Quantification has been finished.
2021-07-20 07:45:00,115 Running Salmon using Snakemake
2021-07-20 07:45:00,366 Lock 4378001808 acquired on /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmpd0rnswwisnakemake-runtime-source-cache/aacb3f05655970a320900b0dd13afa984b937a586ed442e59223e95ebfacd6b6.lock
2021-07-20 07:45:00,367 Lock 4378001808 released on /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmpd0rnswwisnakemake-runtime-source-cache/aacb3f05655970a320900b0dd13afa984b937a586ed442e59223e95ebfacd6b6.lock
/Users/xwang/Desktop/software/SalmonTE/snakemake/Snakefile.paired:103: SyntaxWarning: "is" with a literal. Did you mean "=="?
Job stats:
job count min threads max threads
------------------- ------- ------------- -------------
all 1 1 1
collect_abundance 1 1 1
collect_mappability 1 1 1
run_salmon_fq 4 1 1
total 7 1 1
2021-07-20 07:45:00,454 Job stats:
job count min threads max threads
------------------- ------- ------------- -------------
all 1 1 1
collect_abundance 1 1 1
collect_mappability 1 1 1
run_salmon_fq 4 1 1
total 7 1 1
/bin/bash: line 1: 35133 Abort trap: 6 /Users/xwang/Desktop/software/SalmonTE/salmon/darwin/bin/salmon quant -q -i /Users/xwang/Desktop/software/SalmonTE/reference/hs -l A -1 /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmp_lp_l6lr/TARDBP_1_R1.fastq -2 /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmp_lp_l6lr/TARDBP_1_R2.fastq -o /Users/xwang/Desktop/software/SalmonTE/SalmonTE_output/TARDBP_1 -p 4 2> /dev/null
[Tue Jul 20 07:45:00 2021]
2021-07-20 07:45:00,649 [Tue Jul 20 07:45:00 2021]
Error in rule run_salmon_fq:
2021-07-20 07:45:00,650 Error in rule run_salmon_fq:
jobid: 5
2021-07-20 07:45:00,650 jobid: 5
output: /Users/xwang/Desktop/software/SalmonTE/SalmonTE_output/TARDBP_1
2021-07-20 07:45:00,650 output: /Users/xwang/Desktop/software/SalmonTE/SalmonTE_output/TARDBP_1
shell:
/Users/xwang/Desktop/software/SalmonTE/salmon/darwin/bin/salmon quant -q -i /Users/xwang/Desktop/software/SalmonTE/reference/hs -l A -1 /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmp_lp_l6lr/TARDBP_1_R1.fastq -2 /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmp_lp_l6lr/TARDBP_1_R2.fastq -o /Users/xwang/Desktop/software/SalmonTE/SalmonTE_output/TARDBP_1 -p 4 2>/dev/null
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
2021-07-20 07:45:00,650 shell:
/Users/xwang/Desktop/software/SalmonTE/salmon/darwin/bin/salmon quant -q -i /Users/xwang/Desktop/software/SalmonTE/reference/hs -l A -1 /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmp_lp_l6lr/TARDBP_1_R1.fastq -2 /var/folders/43/wqcsdbhd3vs8wpxp0903j0g40000gp/T/tmp_lp_l6lr/TARDBP_1_R2.fastq -o /Users/xwang/Desktop/software/SalmonTE/SalmonTE_output/TARDBP_1 -p 4 2>/dev/null
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
2021-07-20 07:45:00,650
Exiting because a job execution failed. Look above for error message
2021-07-20 07:45:00,652 Exiting because a job execution failed. Look above for error message
Traceback (most recent call last):
File "/Users/xwang/Desktop/software/SalmonTE/SalmonTE.py", line 292, in <module>
run(args)
File "/Users/xwang/Desktop/software/SalmonTE/SalmonTE.py", line 243, in run
run_salmon(param)
File "/Users/xwang/Desktop/software/SalmonTE/SalmonTE.py", line 156, in run_salmon
with open(os.path.join(param["--outpath"], "EXPR.csv" ), "r") as inp:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/xwang/Desktop/software/SalmonTE/SalmonTE_output/EXPR.csv'@Xiaofei-git are you running this on macOS?
Hyun-Hwan Jeong
Xiaofei-git
commented
2 years ago @Xiaofei-git are you running this on macOS?
Hyun-Hwan Jeong
Yes.
hyunhwan-jeong
commented
2 years ago @Xiaofei-git,
You may execute the line before you run SalmonTE
export DYLD_LIBRARY_PATH=/Users/xwang/Desktop/software/SalmonTE/salmon/darwin/libOr you can add the command to your shell configuration (e.g., .bashrc).
Hope it helps,
Hyun-Hwan Jeong
Xiaofei-git
commented
2 years ago @Xiaofei-git,
You may execute the line before you run SalmonTE
export DYLD_LIBRARY_PATH=/Users/xwang/Desktop/software/SalmonTE/salmon/darwin/libOr you can add the command to your shell configuration (e.g.,
.bashrc).Hope it helps,
Hyun-Hwan Jeong
Thanks a lot!
Dear there,
I tried to install SalmonTE. But, I failed to make it run on test data and did't figure out why did it happen.
Really appreciate for any help!
Best,
Xiaofei