Closed brunocontrerasmoreira closed 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
It's a known issue and on our to do list. Thank you
Operating system Debian GNU/Linux 11 (bullseye)
Package name ipa (wrapper) version=1.8.0
Conda environment
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:
Error message
To Fix