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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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Stuck at the "Cleaning Genome" phase #104

Closed rpianezza closed 6 months ago

rpianezza commented 6 months ago

Hi Toby, I get this error message when running EarlGrey:

<<< Cleaning Genome >>>

/home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 3: import: command not found /home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 4: import: command not found /home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 6: args: command not found /home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 8: dictionary: command not found /home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 9: fastaIn: command not found /home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 11: syntax error near unexpected token (' /home/riccardo/repeatannotation/EarlGrey/scripts/faswap.py: line 11:a=dict(csv.reader(open(dictionary),delimiter="\t"))'

Do you have any idea of what's going on here?

TobyBaril commented 6 months ago

Hi!

This is odd...how did you install Earl Grey? Are you using a conda install? any information on version and OS would be helpful. In this case it is struggling to run the script and can't find python commands, so looks like it is trying to execute the script as a bash script for some reason...

rpianezza commented 6 months ago

I installed EarlGrey cloning the repository and running the "configure" file, since I already had RepeatMasker and RepeatModeler. I looked back at the installation log file, and I found this error which I think is the reason for the error above:

Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 111, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda_env/installers/conda.py", line 32, in install
    prune=getattr(args, 'prune', False), update_modifier=UpdateModifier.FREEZE_INSTALLED)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
    ssc = self._run_sat(ssc)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 808, in _run_sat
    should_retry_solve=ssc.should_retry_solve
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/resolve.py", line 1318, in solve
    self.find_conflicts(specs, specs_to_add, history_specs)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/resolve.py", line 347, in find_conflicts
    bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/resolve.py", line 507, in build_conflict_map
    root, search_node, dep_graph, num_occurances)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/resolve.py", line 369, in breadth_first_search_for_dep_graph
    last_spec = MatchSpec.union((path[-1], target_paths[-1][-1]))[0]
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 481, in union
    return cls.merge(match_specs, union=True)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in merge
    reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in <lambda>
    reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 502, in _merge
    final = this_component.union(that_component)
  File "/home/riccardo/anaconda3/lib/python3.7/site-packages/conda/models/match_spec.py", line 764, in union
    return '|'.join(options)
TypeError: sequence item 0: expected str instance, Channel found

$ /home/riccardo/anaconda3/bin/conda-env create -f ./earlGrey.yml

I already tried to reinstall conda from scratches after removing all of Earl Grey files, got the same error

TobyBaril commented 6 months ago

Ah okay, I would suggest making a totally new environment with this yml (save as earlgrey.yml...or whatever...):

name: earlgrey
channels:
  - bioconda
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_13
  - anyio=4.0.0=pyhd8ed1ab_0
  - argcomplete=3.1.2=pyhd8ed1ab_0
  - argon2-cffi=23.1.0=pyhd8ed1ab_0
  - argon2-cffi-bindings=21.2.0=py39hd1e30aa_4
  - arrow=1.3.0=pyhd8ed1ab_0
  - arrow-cpp=10.0.1=h3e2b116_4_cpu
  - asttokens=2.4.0=pyhd8ed1ab_0
  - async-lru=2.0.4=pyhd8ed1ab_0
  - async_generator=1.10=py_0
  - attrs=23.1.0=pyh71513ae_1
  - aws-c-auth=0.6.21=hd93a3ba_3
  - aws-c-cal=0.5.20=hd3b2fe5_3
  - aws-c-common=0.8.5=h166bdaf_0
  - aws-c-compression=0.2.16=hf5f93bc_0
  - aws-c-event-stream=0.2.17=h57874a7_1
  - aws-c-http=0.7.0=h96ef541_0
  - aws-c-io=0.13.12=h57ca295_1
  - aws-c-mqtt=0.7.13=h0b5698f_12
  - aws-c-s3=0.2.1=h5d7e488_4
  - aws-c-sdkutils=0.1.7=hf5f93bc_0
  - aws-checksums=0.1.14=h6027aba_0
  - aws-crt-cpp=0.18.16=h26430d7_8
  - aws-sdk-cpp=1.9.379=h56135f1_7
  - babel=2.13.0=pyhd8ed1ab_0
  - backcall=0.2.0=pyh9f0ad1d_0
  - backports=1.0=pyhd8ed1ab_3
  - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
  - beautifulsoup4=4.12.2=pyha770c72_0
  - bedtools=2.31.0=hf5e1c6e_3
  - binutils_impl_linux-64=2.40=hf600244_0
  - binutils_linux-64=2.40=hbdbef99_2
  - bioconductor-biobase=2.58.0=r42ha9d7317_1
  - bioconductor-biocgenerics=0.44.0=r42hdfd78af_0
  - bioconductor-biocio=1.8.0=r42hdfd78af_0
  - bioconductor-biocparallel=1.32.5=r42hf17093f_1
  - bioconductor-biostrings=2.66.0=r42ha9d7317_1
  - bioconductor-bsgenome=1.66.3=r42hdfd78af_0
  - bioconductor-data-packages=20230718=hdfd78af_1
  - bioconductor-delayedarray=0.24.0=r42ha9d7317_1
  - bioconductor-genomeinfodb=1.34.9=r42hdfd78af_0
  - bioconductor-genomeinfodbdata=1.2.9=r42hdfd78af_0
  - bioconductor-genomicalignments=1.34.0=r42ha9d7317_1
  - bioconductor-genomicranges=1.50.0=r42ha9d7317_1
  - bioconductor-iranges=2.32.0=r42ha9d7317_1
  - bioconductor-matrixgenerics=1.10.0=r42hdfd78af_0
  - bioconductor-plyranges=1.18.0=r42hdfd78af_0
  - bioconductor-rhtslib=2.0.0=r42ha9d7317_1
  - bioconductor-rsamtools=2.14.0=r42hf17093f_1
  - bioconductor-rtracklayer=1.58.0=r42h171f361_1
  - bioconductor-s4vectors=0.36.0=r42ha9d7317_1
  - bioconductor-summarizedexperiment=1.28.0=r42hdfd78af_0
  - bioconductor-xvector=0.38.0=r42ha9d7317_1
  - bioconductor-zlibbioc=1.44.0=r42ha9d7317_2
  - biopython=1.81=py39h72bdee0_0
  - blast=2.14.1=pl5321h6f7f691_0
  - bleach=6.1.0=pyhd8ed1ab_0
  - blosc=1.21.5=h0f2a231_0
  - brotli=1.0.9=h166bdaf_9
  - brotli-bin=1.0.9=h166bdaf_9
  - brotli-python=1.0.9=py39h5a03fae_9
  - brotlipy=0.7.0=py39hd1e30aa_1006
  - bwidget=1.9.14=ha770c72_1
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.20.1=hd590300_0
  - c-blosc2=2.10.5=hb4ffafa_0
  - ca-certificates=2024.2.2=hbcca054_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cairo=1.16.0=ha61ee94_1014
  - cd-hit=4.8.1=h43eeafb_9
  - certifi=2024.2.2=pyhd8ed1ab_0
  - cffi=1.16.0=py39h7a31438_0
  - chardet=5.2.0=py39hf3d152e_1
  - charset-normalizer=3.3.0=pyhd8ed1ab_0
  - click=8.1.7=unix_pyh707e725_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - comm=0.1.4=pyhd8ed1ab_0
  - contourpy=1.1.1=py39h7633fee_1
  - cryptography=39.0.0=py39hd598818_0
  - curl=7.87.0=h6312ad2_0
  - cycler=0.12.1=pyhd8ed1ab_0
  - debugpy=1.8.0=py39h3d6467e_1
  - decorator=5.1.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - dnspython=2.4.2=pyhd8ed1ab_0
  - emboss=6.6.0=hf2fadf7_7
  - entrez-direct=16.2=he881be0_1
  - entrypoints=0.4=pyhd8ed1ab_0
  - exceptiongroup=1.1.3=pyhd8ed1ab_0
  - executing=1.2.0=pyhd8ed1ab_0
  - expat=2.5.0=hcb278e6_1
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=hab24e00_0
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.43.1=py39hd1e30aa_0
  - fqdn=1.5.1=pyhd8ed1ab_0
  - freetype=2.12.1=h267a509_2
  - fribidi=1.0.10=h36c2ea0_0
  - future=0.18.3=pyhd8ed1ab_0
  - gcc_impl_linux-64=13.2.0=h338b0a0_2
  - gcc_linux-64=13.2.0=h112eaf3_2
  - gettext=0.21.1=h27087fc_0
  - gflags=2.2.2=he1b5a44_1004
  - gfortran_impl_linux-64=13.2.0=h76e1118_2
  - gfortran_linux-64=13.2.0=hcfe307d_2
  - giflib=5.2.1=h0b41bf4_3
  - glib=2.78.0=hfc55251_0
  - glib-tools=2.78.0=hfc55251_0
  - glog=0.6.0=h6f12383_0
  - gmp=6.2.1=h58526e2_0
  - graphite2=1.3.13=h58526e2_1001
  - gsl=2.7=he838d99_0
  - gxx_impl_linux-64=13.2.0=h338b0a0_2
  - gxx_linux-64=13.2.0=hc53e3bf_2
  - h11=0.14.0=pyhd8ed1ab_0
  - h2=4.1.0=pyhd8ed1ab_0
  - h5py=3.9.0=nompi_py39h4dfffb9_100
  - harfbuzz=6.0.0=h8e241bc_0
  - hdf5=1.14.0=nompi_h5231ba7_103
  - hpack=4.0.0=pyh9f0ad1d_0
  - htseq=2.0.3=py39hd5189a5_1
  - httpcore=1.0.0=pyhd8ed1ab_0
  - hyperframe=6.0.1=pyhd8ed1ab_0
  - icu=70.1=h27087fc_0
  - idna=3.4=pyhd8ed1ab_0
  - importlib-metadata=6.8.0=pyha770c72_0
  - importlib-resources=6.1.0=pyhd8ed1ab_0
  - importlib_metadata=6.8.0=hd8ed1ab_0
  - importlib_resources=6.1.0=pyhd8ed1ab_0
  - ipykernel=6.25.2=pyh2140261_0
  - ipython=8.16.1=pyh0d859eb_0
  - ipython_genutils=0.2.0=py_1
  - isoduration=20.11.0=pyhd8ed1ab_0
  - jbig=2.1=h7f98852_2003
  - jedi=0.19.1=pyhd8ed1ab_0
  - jinja2=3.1.2=pyhd8ed1ab_1
  - jpeg=9e=h0b41bf4_3
  - jq=1.6=h36c2ea0_1000
  - json5=0.9.14=pyhd8ed1ab_0
  - jsonpointer=2.4=py39hf3d152e_3
  - jsonschema=4.19.1=pyhd8ed1ab_0
  - jsonschema-specifications=2023.7.1=pyhd8ed1ab_0
  - jsonschema-with-format-nongpl=4.19.1=pyhd8ed1ab_0
  - jupyter-lsp=2.2.0=pyhd8ed1ab_0
  - jupyter_client=8.4.0=pyhd8ed1ab_0
  - jupyter_core=5.4.0=py39hf3d152e_0
  - jupyter_events=0.7.0=pyhd8ed1ab_2
  - jupyter_server=2.7.3=pyhd8ed1ab_1
  - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
  - jupyterlab=4.0.7=pyhd8ed1ab_0
  - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
  - jupyterlab_server=2.25.0=pyhd8ed1ab_0
  - kernel-headers_linux-64=4.18.0=he073ed8_0
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.5=py39h7633fee_1
  - krb5=1.20.1=hf9c8cef_0
  - lcms2=2.14=h6ed2654_0
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libabseil=20220623.0=cxx17_h05df665_6
  - libaec=1.1.2=h59595ed_1
  - libarrow=10.0.1=hee49ebd_4_cpu
  - libblas=3.9.0=18_linux64_openblas
  - libbrotlicommon=1.0.9=h166bdaf_9
  - libbrotlidec=1.0.9=h166bdaf_9
  - libbrotlienc=1.0.9=h166bdaf_9
  - libcblas=3.9.0=18_linux64_openblas
  - libcrc32c=1.1.2=h9c3ff4c_0
  - libcurl=7.87.0=h6312ad2_0
  - libdeflate=1.13=h166bdaf_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libevent=2.1.10=h9b69904_4
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-devel_linux-64=13.2.0=ha9c7c90_2
  - libgcc-ng=13.2.0=h807b86a_2
  - libgd=2.3.3=h18fbbfe_3
  - libgfortran-ng=13.2.0=h69a702a_2
  - libgfortran5=13.2.0=ha4646dd_2
  - libglib=2.78.0=hebfc3b9_0
  - libgomp=13.2.0=h807b86a_2
  - libgoogle-cloud=2.5.0=h5d50b59_1
  - libgrpc=1.51.1=h05bd8bd_0
  - libiconv=1.17=h166bdaf_0
  - libidn2=2.3.4=h166bdaf_0
  - liblapack=3.9.0=18_linux64_openblas
  - libnghttp2=1.51.0=hdcd2b5c_0
  - libnsl=2.0.0=hd590300_1
  - libopenblas=0.3.24=pthreads_h413a1c8_0
  - libpng=1.6.39=h753d276_0
  - libprotobuf=3.21.12=hfc55251_2
  - libsanitizer=13.2.0=h7e041cc_2
  - libsodium=1.0.18=h36c2ea0_1
  - libsqlite=3.43.2=h2797004_0
  - libssh2=1.10.0=haa6b8db_3
  - libstdcxx-devel_linux-64=13.2.0=ha9c7c90_2
  - libstdcxx-ng=13.2.0=h7e041cc_2
  - libthrift=0.16.0=h491838f_2
  - libtiff=4.4.0=h0e0dad5_3
  - libunistring=0.9.10=h7f98852_0
  - libutf8proc=2.8.0=h166bdaf_0
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp=1.2.4=h522a892_0
  - libwebp-base=1.2.4=h166bdaf_0
  - libxcb=1.13=h7f98852_1004
  - libxml2=2.10.3=hca2bb57_4
  - libzlib=1.2.13=hd590300_5
  - lz4-c=1.9.4=hcb278e6_0
  - lzo=2.10=h516909a_1000
  - mafft=7.520=h031d066_2
  - make=4.3=hd18ef5c_1
  - markupsafe=2.1.3=py39hd1e30aa_1
  - matplotlib-base=3.8.0=py39he9076e7_2
  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
  - mgkit=0.5.8=py39hf95cd2a_1
  - mistune=3.0.1=pyhd8ed1ab_0
  - mock=5.1.0=pyhd8ed1ab_0
  - mreps=2.6.01=h031d066_4
  - msgpack-python=1.0.6=py39h7633fee_0
  - munkres=1.1.4=pyh9f0ad1d_0
  - natsort=8.4.0=pyhd8ed1ab_0
  - nbclient=0.8.0=pyhd8ed1ab_0
  - nbconvert=7.9.2=pyhd8ed1ab_0
  - nbconvert-core=7.9.2=pyhd8ed1ab_0
  - nbconvert-pandoc=7.9.2=pyhd8ed1ab_0
  - nbformat=5.9.2=pyhd8ed1ab_0
  - ncbi-vdb=3.0.0=pl5321h87f3376_0
  - ncls=0.0.68=py39hf95cd2a_1
  - ncurses=6.4=hcb278e6_0
  - nest-asyncio=1.5.8=pyhd8ed1ab_0
  - networkx=3.1=pyhd8ed1ab_0
  - nomkl=1.0=h5ca1d4c_0
  - notebook=7.0.4=pyhd8ed1ab_0
  - notebook-shim=0.2.3=pyhd8ed1ab_0
  - numexpr=2.8.7=py39hb68c0d3_103
  - numpy=1.26.0=py39h474f0d3_0
  - olefile=0.46=pyh9f0ad1d_1
  - oniguruma=6.9.8=h166bdaf_0
  - openjpeg=2.5.0=h7d73246_1
  - openssl=1.1.1w=hd590300_0
  - orc=1.8.2=hfdbbad2_2
  - overrides=7.4.0=pyhd8ed1ab_0
  - packaging=23.2=pyhd8ed1ab_0
  - pandas=2.1.1=py39hddac248_1
  - pandoc=3.1.3=h32600fe_0
  - pandocfilters=1.5.0=pyhd8ed1ab_0
  - pango=1.50.14=hd33c08f_0
  - parallel=20230922=ha770c72_0
  - parquet-cpp=1.5.1=2
  - parso=0.8.3=pyhd8ed1ab_0
  - patsy=0.5.3=pyhd8ed1ab_0
  - pcre=8.45=h9c3ff4c_0
  - pcre2=10.40=hc3806b6_0
  - perl=5.32.1=4_hd590300_perl5
  - perl-app-cpanminus=1.7047=pl5321hd8ed1ab_0
  - perl-archive-tar=2.40=pl5321hdfd78af_0
  - perl-base=2.23=pl5321hd8ed1ab_0
  - perl-business-isbn=3.007=pl5321hd8ed1ab_0
  - perl-business-isbn-data=20210112.006=pl5321hd8ed1ab_0
  - perl-carp=1.50=pl5321hd8ed1ab_0
  - perl-common-sense=3.75=pl5321hd8ed1ab_0
  - perl-compress-raw-bzip2=2.201=pl5321h166bdaf_0
  - perl-compress-raw-zlib=2.202=pl5321h166bdaf_0
  - perl-constant=1.33=pl5321hd8ed1ab_0
  - perl-data-dumper=2.183=pl5321h166bdaf_0
  - perl-devel-size=0.83=pl5321h031d066_4
  - perl-digest-hmac=1.04=pl5321hdfd78af_0
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  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.8.4=h0b41bf4_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-libxt=1.3.0=hd590300_0
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - yq=3.2.3=pyhd8ed1ab_0
  - zeromq=4.3.5=h59595ed_0
  - zipp=3.17.0=pyhd8ed1ab_0
  - zlib=1.2.13=hd590300_5
  - zlib-ng=2.0.7=h0b41bf4_0
  - zstd=1.5.5=hfc55251_0

Then run:

conda env create -f ./earlgrey.yml
rpianezza commented 6 months ago

Unfortunately I get always the same installation problem. I looked around in the internet for possible solutions but I'm still stucked. Anyway, it doesn't look like an EarlGrey problem, but more a Conda problem

TobyBaril commented 6 months ago

Ah yes it looks to be an issue with your conda install. Do you have access to mamba, sometimes it is better at resolving issues like this?

rpianezza commented 6 months ago

In the end I solved the problem using the Docker image instead of trying installing with conda. Now it is running properly

TobyBaril commented 6 months ago

Great! Thanks for the update!