command not found for inital concoct steps

[lyisrae1]

Using Miniconda 23.11.0
Linux

Hello,

Thank you for reading this and answering my query.
I have been trying to use concoct, but it is giving me a bit of an issue. I was finally able to download it on miniconda, but it does not recognize the commands in the first two steps of the workflow: "cut_up_fasta.py" or "concoct_coverage_table.py"

I tried updating concoct, but it said that the program was fully updated. Can you please tell me what I'm doing wrong? Here are all of the packages inside my "bins" environment:

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
alabaster 0.7.12 pyhd3eb1b0_0
asn1crypto 1.4.0 py_0
babel 2.9.0 pyhd3eb1b0_0
biopython 1.68 py27_0 bioconda
blas 1.0 openblas
ca-certificates 2024.9.24 h06a4308_0
certifi 2020.6.20 pyhd3eb1b0_3
cffi 1.14.0 py27he30daa8_1
chardet 3.0.4 py27_1003
concoct 0.4.2 py27hd1ccf6d_0 bioconda
cryptography 2.8 py27h1ba5d50_0
cython 0.29.14 py27he6710b0_0
docutils 0.15.2 py27_0
enum34 1.1.6 py27_1
freetype 2.12.1 h4a9f257_0
gsl 2.2.1 h0c605f7_3
idna 2.10 pyhd3eb1b0_0
imagesize 1.2.0 pyhd3eb1b0_0
ipaddress 1.0.23 py_0
jinja2 2.11.3 pyhd3eb1b0_0
jpeg 9e h5eee18b_3
lerc 3.0 h295c915_0
libdeflate 1.17 h5eee18b_1
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 11.2.0 h1234567_1
libopenblas 0.2.20 h9ac9557_7
libpng 1.6.39 h5eee18b_0
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.5.1 h6a678d5_0
libwebp-base 1.3.2 h5eee18b_1
lz4-c 1.9.4 h6a678d5_1
markupsafe 1.1.1 py27h7b6447c_0
mmtf-python 1.0.2 py27_0 bioconda
msgpack-python 0.6.1 py27hfd86e86_1
ncurses 6.4 h6a678d5_0
nose 1.3.7 py27_2
numpy 1.15.0 py27h2aefc1b_0
numpy-base 1.15.0 py27h7cdd4dd_0
olefile 0.46 pyhd3eb1b0_0
openblas 0.2.20 7
openblas-devel 0.2.20 7
openssl 1.1.1w h7f8727e_0
packaging 20.9 pyhd3eb1b0_0
pandas 0.24.2 py27he6710b0_0
pillow 6.2.1 py27h34e0f95_0
pip 19.3.1 py27_0
pycparser 2.20 py_2
pygments 2.5.2 py_0
pyopenssl 20.0.1 pyhd3eb1b0_1
pyparsing 2.4.7 pyhd3eb1b0_0
pysocks 1.7.1 py27_0
python 2.7.18 ha1903f6_2
python-dateutil 2.8.2 pyhd3eb1b0_0
pytz 2021.3 pyhd3eb1b0_0
readline 8.2 h5eee18b_0
reportlab 3.5.26 py27he686d34_0
requests 2.25.1 pyhd3eb1b0_0
scikit-learn 0.19.1 py27_nomklh6cfcb94_0
scipy 1.1.0 py27_nomklh9c1e066_0
setuptools 44.0.0 py27_0
six 1.16.0 pyhd3eb1b0_1
snowballstemmer 2.1.0 pyhd3eb1b0_0
sphinx 1.8.5 py27_0
sphinx_rtd_theme 0.4.3 pyhd3eb1b0_0
sphinxcontrib 1.0 py27_1
sphinxcontrib-websupport 1.2.4 py_0
sqlite 3.45.3 h5eee18b_0
tk 8.6.14 h39e8969_0
typing 3.5.2.2 py27_0 bioconda
urllib3 1.25.7 py27_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.4.6 h5eee18b_1
zlib 1.2.13 h5eee18b_1
zstd 1.5.6 hc292b87_0

I am also inputting the code I used for my installation process, and the two different ways I tried to use concoct:
start-conda
1.
conda activate bins
cut_up_fasta.py /scratch/public/genomics/yisraell/88_more-kmers_contigs.fasta -c 10000 -o 0 --merge_last -b /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.bed > /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.fa
concoct_coverage_table.py /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.bed /scratch/public/genomics/yisraell/Concoct/88_more-kmers_sorted.bam > /scratch/public/genomics/yisraell/Concoct/88_more-kmers_coverage_table.tsv
conda deactivate
conda deactivate

conda activate bins
concoct cut_up_fasta.py /scratch/public/genomics/yisraell/88_more-kmers_contigs.fasta -c 10000 -o 0 --merge_last -b /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.bed > /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.fa
concoct concoct_coverage_table.py /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.bed /scratch/public/genomics/yisraell/Concoct/88_more-kmers_sorted.bam > /scratch/public/genomics/yisraell/Concoct/88_more-kmers_coverage_table.tsv
conda deactivate
conda deactivate

ERRORS:

1. /cm/local/apps/uge/var/spool/compute-65-13/job_scripts/3758931: line 24: cut_up_fasta.py: command not found
   /cm/local/apps/uge/var/spool/compute-65-13/job_scripts/3758931: line 25: concoct_coverage_table.py: command not found

2. usage: concoct [-h] [--coverage_file COVERAGE_FILE]
   [--composition_file COMPOSITION_FILE] [-c CLUSTERS]
   [-k KMER_LENGTH] [-l LENGTH_THRESHOLD] [-r READ_LENGTH]
   [--total_percentage_pca TOTAL_PERCENTAGE_PCA] [-b BASENAME]
   [-s SEED] [-i ITERATIONS] [-e EPSILON] [--no_cov_normalization]
   [--no_total_coverage] [--no_original_data] [-o] [-d] [-v]
   concoct: error: unrecognized arguments: cut_up_fasta.py /scratch/public/genomics/yisraell/88_more-kmers_contigs.fasta 0 --merge_last
   usage: concoct [-h] [--coverage_file COVERAGE_FILE]
   [--composition_file COMPOSITION_FILE] [-c CLUSTERS]
   [-k KMER_LENGTH] [-l LENGTH_THRESHOLD] [-r READ_LENGTH]
   [--total_percentage_pca TOTAL_PERCENTAGE_PCA] [-b BASENAME]
   [-s SEED] [-i ITERATIONS] [-e EPSILON] [--no_cov_normalization]
   [--no_total_coverage] [--no_original_data] [-o] [-d] [-v]
   concoct: error: unrecognized arguments: concoct_coverage_table.py /scratch/public/genomics/yisraell/Concoct/88_more-kmers_contigs_10K.bed /scratch/public/genomics/yisraell/Concoct/88_more-kmers_sorted.bam

Thanks,
Leone