KeyError of "calculate_coverage" in multi-sample binning

[KageyamaTakuya]

Hi developers.

I tried multi-sample binning for PacBio 4 samples in conda environment.
But, an error occurred;

(SemiBin) evolution@Threadripper64:/media/evolution/a4be100a-3b42-460a-9f01-9948fb54741e/Kageyama/241104_soil_pacbio$ SemiBin2 multi_easy_bin \
--sequencing-type long_read \
--threads ${CPU} \
--engine cpu \
-i 03_binning/SemiBin2/concatenated.fa.gz \
-b 02_mapping/m84142_240924_053830_s2.bam 02_mapping/m84142_240924_073752_s3.bam 02_mapping/m84142_240924_093700_s4.bam 02_mapping/m84142_240924_113625_s1.bam \
-o 03_binning/SemiBin2/multi_output
2024-12-03 13:48:03 Threadripper64 SemiBin[34927] INFO Binning for long_read
2024-12-03 13:48:03 Threadripper64 SemiBin[34927] INFO SemiBin will run in self supervised mode
2024-12-03 13:48:04 Threadripper64 SemiBin[34927] INFO Running with CPU.
2024-12-03 13:48:04 Threadripper64 SemiBin[34927] INFO Performing multi-sample binning
2024-12-03 13:48:04 Threadripper64 SemiBin[34927] INFO Generating training data...
2024-12-03 13:50:45 Threadripper64 SemiBin[34927] INFO Calculating coverage for every sample.
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/site-packages/SemiBin/generate_coverage.py", line 100, in generate_cov
    contig_cov, must_link_contig_cov = calculate_coverage(
                                       ^^^^^^^^^^^^^^^^^^^
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/site-packages/SemiBin/generate_coverage.py", line 45, in calculate_coverage
    cov_threshold = contig_threshold_dict[sample_name]
                    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
KeyError: 's0.ctg000001l'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/evolution/miniforge3/envs/SemiBin/bin/SemiBin2", line 10, in <module>
    sys.exit(main2())
             ^^^^^^^
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/site-packages/SemiBin/main.py", line 1610, in main2
    multi_easy_binning(
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/site-packages/SemiBin/main.py", line 1313, in multi_easy_binning
    sample_list = generate_sequence_features_multi(logger, args)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/site-packages/SemiBin/main.py", line 964, in generate_sequence_features_multi
    s = r.get()
        ^^^^^^^
  File "/home/evolution/miniforge3/envs/SemiBin/lib/python3.12/multiprocessing/pool.py", line 774, in get
    raise self._value
KeyError: 's0.ctg000001l'

And library information are here;

# packages in environment at /home/evolution/miniforge3/envs/SemiBin:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
arpack                    3.9.1           nompi_h77f6705_101    conda-forge
bedtools                  2.31.1               hf5e1c6e_2    bioconda
bowtie2                   2.5.4                h7071971_4    bioconda
brotli-python             1.1.0           py312h2ec8cdc_2    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.2               heb4867d_0    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312h06ac9bb_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
coloredlogs               15.0.1             pyhd8ed1ab_3    conda-forge
filelock                  3.16.1             pyhd8ed1ab_0    conda-forge
fsspec                    2024.10.0          pyhff2d567_0    conda-forge
gawk                      5.3.1                hcd3d067_0    conda-forge
gettext                   0.22.5               he02047a_3    conda-forge
gettext-tools             0.22.5               he02047a_3    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
gmpy2                     2.1.5           py312h7201bc8_2    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hmmer                     3.4                  hdbdd923_2    bioconda
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
htslib                    1.21                 h5efdd21_0    bioconda
humanfriendly             10.0               pyhd8ed1ab_6    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
libabseil                 20240116.2      cxx17_he02047a_1    conda-forge
libasprintf               0.22.5               he8f35ee_3    conda-forge
libasprintf-devel         0.22.5               he8f35ee_3    conda-forge
libblas                   3.9.0           25_linux64_openblas    conda-forge
libcblas                  3.9.0           25_linux64_openblas    conda-forge
libcurl                   8.8.0                hca28451_1    conda-forge
libdeflate                1.21                 h4bc722e_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.3                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgettextpo              0.22.5               he02047a_3    conda-forge
libgettextpo-devel        0.22.5               he02047a_3    conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran-ng            14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libidn2                   2.3.7                hd590300_0    conda-forge
liblapack                 3.9.0           25_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libprotobuf               4.25.3               h08a7969_0    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libtorch                  2.4.1           cpu_generic_hb3b73e9_0    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.49.2               hb9d3cd8_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               hc051c1a_1    conda-forge
libzlib                   1.2.13               h4ab18f5_6    conda-forge
markupsafe                3.0.2           py312h178313f_0    conda-forge
mmseqs2                   13.45111        pl5321hf1761c0_2    bioconda
mpc                       1.3.1                h24ddda3_1    conda-forge
mpfr                      4.2.1                h90cbb55_3    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  he02047a_1    conda-forge
networkx                  3.4.2              pyhd8ed1ab_1    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
numexpr                   2.10.1          py312h6a710ac_103    conda-forge
numpy                     2.1.3           py312h58c1407_0    conda-forge
openssl                   3.3.2                hb9d3cd8_0    conda-forge
pandas                    2.2.3           py312hf9745cd_1    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
pip                       24.3.1             pyh8b19718_0    conda-forge
prodigal                  2.6.3                h031d066_9    bioconda
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.12.3          hab00c5b_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-igraph             0.11.5          py312h4f72774_1    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python_abi                3.12                    5_cp312    conda-forge
pytorch                   2.4.1           cpu_generic_py312h411db4e_0    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2           py312h66e93f0_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
samtools                  1.21                 h50ea8bc_0    bioconda
scikit-learn              1.5.2           py312h7a48858_1    conda-forge
scipy                     1.14.1          py312h62794b6_1    conda-forge
semibin                   2.1.0              pyhdfd78af_0    bioconda
setuptools                75.3.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleef                     3.7                  h1b44611_0    conda-forge
sympy                     1.13.3          pypyh2585a3b_103    conda-forge
texttable                 1.7.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tqdm                      4.66.6             pyhd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
urllib3                   2.2.3              pyhd8ed1ab_0    conda-forge
wget                      1.21.4               hda4d442_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zlib                      1.2.13               h4ab18f5_6    conda-forge
zstandard                 0.23.0          py312hef9b889_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Do you have any idea to solve this?

Thanks