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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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time: command not found #614

Closed brunocontrerasmoreira closed 10 months ago

brunocontrerasmoreira commented 10 months ago

Operating system Debian GNU/Linux 11 (bullseye)

Package name ipa (wrapper) version=1.8.0

Conda environment

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
amply                     0.1.6              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
brotli-python             1.1.0           py311hb755f60_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.20.1               hd590300_1    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.1              pyhd8ed1ab_0    conda-forge
coin-or-cbc               2.10.10              h9002f0b_0    conda-forge
coin-or-cgl               0.60.7               h516709c_0    conda-forge
coin-or-clp               1.17.8               h1ee7a9c_0    conda-forge
coin-or-osi               0.108.8              ha2443b9_0    conda-forge
coin-or-utils             2.11.9               hee58242_0    conda-forge
coincbc                   2.10.10           0_metapackage    conda-forge
configargparse            1.7                pyhd8ed1ab_0    conda-forge
connection_pool           0.0.3              pyhd3deb0d_0    conda-forge
datrie                    0.8.2           py311h459d7ec_7    conda-forge
docutils                  0.20.1          py311h38be061_2    conda-forge
dpath                     2.1.6              pyha770c72_0    conda-forge
gitdb                     4.0.11             pyhd8ed1ab_0    conda-forge
gitpython                 3.1.40             pyhd8ed1ab_0    conda-forge
htslib                    1.18                 h81da01d_0    bioconda
humanfriendly             10.0               pyhd8ed1ab_6    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib_resources       6.1.0              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.19.1             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jupyter_core              5.4.0           py311h38be061_0    conda-forge
k8                        0.2.5                hdcf5f25_4    bioconda
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libblas                   3.9.0           19_linux64_openblas    conda-forge
libcblas                  3.9.0           19_linux64_openblas    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libdeflate                1.19                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
liblapack                 3.9.0           19_linux64_openblas    conda-forge
liblapacke                3.9.0           19_linux64_openblas    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libsqlite                 3.43.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.3           py311h459d7ec_1    conda-forge
minimap2                  2.26                 he4a0461_2    bioconda
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
networkx                  3.2                pyhd8ed1ab_1    conda-forge
openssl                   3.1.3                hd590300_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pb-falconc                1.15.0               haabb649_2    bioconda
pbipa                     1.8.0                h6ead514_2    bioconda
pcre                      8.45                 h9c3ff4c_0    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
plac                      1.4.0              pyhd8ed1ab_0    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
psutil                    5.9.5           py311h459d7ec_1    conda-forge
pulp                      2.7.0           py311h38be061_1    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.11.6          hab00c5b_0_cpython    conda-forge
python-fastjsonschema     2.18.1             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pyyaml                    6.0.1           py311h459d7ec_1    conda-forge
racon                     1.5.0                h21ec9f0_2    bioconda
readline                  8.2                  h8228510_1    conda-forge
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
reretry                   0.11.8             pyhd8ed1ab_0    conda-forge
rpds-py                   0.10.6          py311h46250e7_0    conda-forge
samtools                  1.18                 h50ea8bc_1    bioconda
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
smart_open                6.4.0              pyhd8ed1ab_0    conda-forge
smmap                     5.0.0              pyhd8ed1ab_0    conda-forge
snakemake-minimal         7.32.4             pyhdfd78af_1    bioconda
stopit                    1.1.2                      py_0    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
throttler                 1.2.2              pyhd8ed1ab_0    conda-forge
time                      1.8                  h516909a_0    conda-forge
tk                        8.6.13               h2797004_0    conda-forge
toposort                  1.10               pyhd8ed1ab_0    conda-forge
traitlets                 5.11.2             pyhd8ed1ab_0    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.0.7              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
wrapt                     1.15.0          py311h459d7ec_1    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yte                       1.5.1              pyha770c72_2    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Describe the bug After install ipa as explained in https://github.com/PacificBiosciences/pbbioconda/wiki/Improved-Phased-Assembler it will stop a few seconds after the job was launched with this command:

ipa local --nthreads 20 --njobs 4 -i bam.fofn

Error message

time: command not found

To Fix

conda install time
armintoepfer commented 10 months ago

It's a known issue and on our to do list. Thank you