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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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pbmm2 - command line parser ERROR: unknown option 'alignment-threads' (and 'sort-threads' and 'secondary') #407

Closed CharlesARoy closed 2 years ago

CharlesARoy commented 3 years ago

Operating system OS: CentOS Linux Version: 7 (Core)

Package name Tool: pbmm2 Version: pbmm2 1.4.0 (commit 1.4.0)

Conda environment

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    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
certifi                   2020.12.5        py38h578d9bd_1    conda-forge
curl                      7.76.1               h979ede3_1    conda-forge
cycler                    0.10.0                     py_2    conda-forge
decorator                 5.0.7              pyhd8ed1ab_0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
htslib                    1.10.2               hd3b49d5_1    bioconda
jpeg                      9d                   h36c2ea0_0    conda-forge
k8                        0.2.5                h9a82719_1    bioconda
kiwisolver                1.3.1            py38h1fd1430_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                9_openblas    conda-forge
libcblas                  3.9.0                9_openblas    conda-forge
libcurl                   7.76.1               hc4aaa36_1    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
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                9_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.15          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libtiff                   4.2.0                hdc55705_1    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
matplotlib-base           3.4.1            py38hcc49a3a_0    conda-forge
minimap2                  2.18                 h5bf99c6_0    bioconda
ncurses                   6.2                  h58526e2_4    conda-forge
networkx                  2.3                        py_0    conda-forge
ngmlr                     0.2.7                h9a82719_3    bioconda
numpy                     1.20.2           py38h9894fe3_0    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
pbmm2                     1.4.0                h56fc30b_0    bioconda
pbsv                      2.6.0                h9ee0642_0    bioconda
pillow                    8.1.2            py38ha0e1e83_1    conda-forge
pip                       21.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pysam                     0.16.0.1         py38hbdc2ae9_1    bioconda
python                    3.8.8           hffdb5ce_0_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
samtools                  1.10                 h2e538c0_3    bioconda
scipy                     1.6.3            py38h7b17777_0    conda-forge
setuptools                49.6.0           py38h578d9bd_3    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sniffles                  1.0.12               h8b12597_1    bioconda
sqlite                    3.35.5               h74cdb3f_0    conda-forge
svim                      1.4.2                      py_0    bioconda
tclap                     1.2.3                h9c3ff4c_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
tornado                   6.1              py38h497a2fe_1    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.9                ha95c52a_0    conda-forge

Describe the bug When I run pbmm2 with some of the descriptive flags listed here, including --alignment-threads, --sort-threads, and --secondary=yes, I get errors like the following:

Error message

terminate called after throwing an instance of '(anonymous namespace)::CommandLineParserException'
  what():  [pbcopper] command line parser ERROR: unknown option 'alignment-threads'

Steps to Reproduce This is private data so I can't provide it, but the command I'm running looks like:

pbmm2 align <reference.fasta> <unaligned_reads.bam> <aligned_reads.bam> --sort --preset SUBREAD --alignment-threads 10 --sort-threads 4 --secondary=yes

Expected behavior Per the documentation, I'd expect these flags to be recognized. Note that for --alignment-threads and --sort-threads I don't get the errors if I use the short flags j and J.

armintoepfer commented 2 years ago

We'll update the docs soon, but in general, please have a look at pbmm2 --help

armintoepfer commented 2 years ago

Will be fixed in the next version