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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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LAA "unsupported sequencing chemistry combination for P6C4" #324

Closed NTNguyen13 closed 4 years ago

NTNguyen13 commented 4 years ago

Operating system Ubuntu 20.04

Package name PBLAA 2.4.2

Conda environment

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
avro-python2              1.9.0                      py_0    bioconda
bam2fastx                 1.3.0                         0    bioconda
bax2bam                   0.0.9                h018d624_7    bioconda
blasr                     5.3.3                h018d624_2    bioconda
blasr_libcpp              5.3.3                h018d624_1    bioconda
brotlipy                  0.7.0           py27h516909a_1000    conda-forge
bzip2                     1.0.8                h516909a_3    conda-forge
c-ares                    1.16.1               h516909a_3    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
certifi                   2019.11.28       py27h8c360ce_1    conda-forge
cffi                      1.14.0           py27hd463f26_0    conda-forge
chardet                   3.0.4           py27h8c360ce_1006    conda-forge
cryptography              2.8              py27h2c19f6a_2    conda-forge
curl                      7.71.1               he644dc0_5    conda-forge
cython                    0.29.15          py27haf22ab1_1    conda-forge
enum34                    1.1.10           py27h8c360ce_1    conda-forge
h5py                      2.10.0          nompi_py27h513d04c_102    conda-forge
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
htslib                    1.9                  h4da6232_3    bioconda
idna                      2.10               pyh9f0ad1d_0    conda-forge
ipaddress                 1.0.23                     py_0    conda-forge
iso8601                   0.1.12                     py_1    conda-forge
krb5                      1.17.1               hfafb76e_2    conda-forge
ld_impl_linux-64          2.34                 hc38a660_9    conda-forge
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcurl                   7.71.1               hcdd3856_5    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         h46ee950_2    conda-forge
libev                     4.33                 h516909a_0    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.3.0               h24d8f2e_16    conda-forge
libgfortran-ng            7.5.0               hdf63c60_16    conda-forge
libgomp                   9.3.0               h24d8f2e_16    conda-forge
liblapack                 3.8.0               17_openblas    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libopenblas               0.3.10          pthreads_hb3c22a3_4    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               hdf63c60_16    conda-forge
lima                      1.11.0                        0    bioconda
linecache2                1.0.0                      py_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.16.5           py27h95a1406_0    conda-forge
openssl                   1.1.1g               h516909a_1    conda-forge
pbalign                   0.3.2                      py_1    bioconda
pbbam                     1.0.6                hc16d5b3_0    bioconda
pbccs                     3.4.0                         0    bioconda
pbcommand                 1.1.1                      py_3    bioconda
pbcopper                  1.6.0                h3e4de3e_0    bioconda
pbcore                    1.7.1                    py27_0    bioconda
pbcoretools               0.2.4                    py27_4    bioconda
pbgcpp                    1.9.0                         0    bioconda
pblaa                     2.4.2                         2    bioconda
pbmm2                     1.3.0                h56fc30b_0    bioconda
pip                       20.1.1             pyh9f0ad1d_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pysam                     0.16.0.1         py27ha863e18_1    bioconda
pysocks                   1.7.1            py27h8c360ce_1    conda-forge
python                    2.7.15          h5a48372_1011_cpython    conda-forge
python_abi                2.7                    1_cp27mu    conda-forge
pytz                      2020.1             pyh9f0ad1d_0    conda-forge
readline                  8.0                  h46ee950_1    conda-forge
requests                  2.24.0             pyh9f0ad1d_0    conda-forge
samtools                  1.9                 h10a08f8_12    bioconda
setuptools                44.0.0                   py27_0    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.32.3               hcee41ef_1    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
traceback2                1.4.0                    py27_0    conda-forge
unittest2                 1.1.0                      py_0    conda-forge
urllib3                   1.25.10                    py_0    conda-forge
wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1009    conda-forge

Describe the bug I run the LAA on the subread bam file (output from bax2bam) from this data: https://github.com/PacificBiosciences/DevNet/wiki/HLA-Multiplexed-GenDx-Amplicons-HLA-A-,-B,--C,--DQB1,-and--DRB1, but encounter the Unsupported sequencing chemistry combination

Error message

>|> 20200831 03:29:45.031 -|- FATAL -|- operator() -|- 0x7fb5b3bab800|| -|- caught exception: "unsupported sequencing chemistry combination:
    binding kit:        100356300
    sequencing kit:     100356200
    basecaller version: 2.3.0.0.140018
"

To Reproduce

  1. Download file from https://github.com/PacificBiosciences/DevNet/wiki/HLA-Multiplexed-GenDx-Amplicons-HLA-A-,-B,--C,--DQB1,-and--DRB1
  2. BAX2BAM the h5 file bax2bam -o pcbio m141109_024645_42142_c100710092550000001823135904221536_s1_p0.1.bax.h5 m141109_024645_42142_c100710092550000001823135904221536_s1_p0.2.bax.h5 m141109_024645_42142_c100710092550000001823135904221536_s1_p0.3.bax.h5
  3. Run LAA on the output file: laa pcbio.subreads.bam

Expected behavior The laa will output the demultiplexed fastq file

armintoepfer commented 4 years ago

RSII data with P6C4 chemistry is no longer supported in the latest LAA. Try your luck using an older LAA version from bioconda, version 2.4.2-2.

Armin