oushujun
An error when running ‘test’, probably related to 'bedtools'
I installed the package with the following script:
cd /home/lcb git clone https://github.com/oushujun/EDTA.git mamba env create -f EDTA_2.2.x.yml
The installation is as follows:
Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge absl-py 2.1.0 pyhd8ed1ab_0 conda-forge aiohttp 3.9.1 py39hd1e30aa_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.8 h166bdaf_0 conda-forge annosine2 1.0.5 pyh7cba7a3_0 bioconda arrow-cpp 11.0.0 ha770c72_5_cpu conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge aws-c-auth 0.6.24 h84a1944_5 conda-forge aws-c-cal 0.5.20 hc60faf5_6 conda-forge aws-c-common 0.8.11 h0b41bf4_0 conda-forge aws-c-compression 0.2.16 h034cb4b_3 conda-forge aws-c-event-stream 0.2.18 h75388cd_6 conda-forge aws-c-http 0.7.4 hf084cc8_2 conda-forge aws-c-io 0.13.17 h10df833_2 conda-forge aws-c-mqtt 0.8.6 hc41645a_6 conda-forge aws-c-s3 0.2.4 h1b8f470_3 conda-forge aws-c-sdkutils 0.1.7 h034cb4b_3 conda-forge aws-checksums 0.1.14 h034cb4b_3 conda-forge aws-crt-cpp 0.19.7 h0073717_7 conda-forge aws-sdk-cpp 1.10.57 h4707e7a_4 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge biopython 1.83 py39hd1e30aa_0 conda-forge blast 2.10.1 pl526he19e7b1_3 bioconda blinker 1.7.0 pyhd8ed1ab_0 conda-forge bokeh 3.3.3 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h166bdaf_9 conda-forge brotli-bin 1.0.9 h166bdaf_9 conda-forge brotli-python 1.0.9 py39h5a03fae_9 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.25.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.2 pyhd8ed1ab_0 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge cd-hit 4.8.1 h43eeafb_9 bioconda certifi 2023.11.17 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py39h7a31438_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.2.0 py39h7633fee_0 conda-forge coreutils 9.4 hd590300_0 conda-forge cryptography 41.0.7 py39he6105cc_1 conda-forge curl 7.88.1 hdc1c0ab_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cytoolz 0.12.2 py39hd1e30aa_1 conda-forge dask 2024.1.0 pyhd8ed1ab_0 conda-forge dask-core 2024.1.0 pyhd8ed1ab_0 conda-forge dill 0.3.7 pyhd8ed1ab_0 conda-forge distributed 2024.1.0 pyhd8ed1ab_0 conda-forge drmaa 0.7.9 py_1000 conda-forge entrez-direct 16.2 he881be0_1 bioconda expat 2.5.0 hcb278e6_1 conda-forge flatbuffers 22.12.06 hcb278e6_2 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_1 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.47.2 py39hd1e30aa_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozenlist 1.4.1 py39hd1e30aa_0 conda-forge fsspec 2023.12.2 pyhca7485f_0 conda-forge gast 0.4.0 pyh9f0ad1d_0 conda-forge gawk 5.3.0 ha916aea_0 conda-forge gcc_impl_linux-64 13.2.0 h338b0a0_3 conda-forge genericrepeatfinder 1.0.2 h4ac6f70_0 bioconda genometools-genometools 1.6.4 py39h58cc16e_0 bioconda gettext 0.21.1 h27087fc_0 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge gfortran_impl_linux-64 13.2.0 h76e1118_3 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge glob2 0.7 py_0 conda-forge glog 0.6.0 h6f12383_0 conda-forge gmp 6.3.0 h59595ed_0 conda-forge google-auth 2.26.2 pyhca7485f_0 conda-forge google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge google-pasta 0.2.0 pyh8c360ce_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpcio 1.51.1 py39he859823_1 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 13.2.0 h338b0a0_3 conda-forge h5py 3.9.0 nompi_py39h4dfffb9_100 conda-forge harfbuzz 6.0.0 h8e241bc_0 conda-forge hdf5 1.14.0 nompi_hb72d44e_103 conda-forge hmmer 3.4 hdbdd923_0 bioconda icu 70.1 h27087fc_0 conda-forge idna 3.6 pyhd8ed1ab_0 conda-forge importlib-metadata 7.0.1 pyha770c72_0 conda-forge importlib-resources 6.1.1 pyhd8ed1ab_0 conda-forge importlib_metadata 7.0.1 hd8ed1ab_0 conda-forge importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge irf 3.08 hdbdd923_0 bioconda isa-l 2.31.0 hd590300_0 conda-forge jinja2 3.1.3 pyhd8ed1ab_0 conda-forge joblib 1.3.2 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge k8 0.2.5 hdcf5f25_4 bioconda keras 2.11.0 pyhd8ed1ab_0 conda-forge keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py39h7633fee_1 conda-forge krb5 1.20.1 h81ceb04_0 conda-forge lcms2 2.15 hfd0df8a_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20220623.0 cxx17_h05df665_6 conda-forge libaec 1.1.2 h59595ed_1 conda-forge libarrow 11.0.0 h2ebd325_5_cpu conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_9 conda-forge libbrotlidec 1.0.9 h166bdaf_9 conda-forge libbrotlienc 1.0.9 h166bdaf_9 conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h36d4200_3 conda-forge libcurl 7.88.1 hdc1c0ab_1 conda-forge libdeflate 1.17 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libevent 2.1.10 h28343ad_4 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 13.2.0 ha9c7c90_103 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgd 2.3.3 h5aea950_4 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libglib 2.78.1 hebfc3b9_0 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libgoogle-cloud 2.7.0 h21dfe5b_1 conda-forge libgrpc 1.51.1 h4fad500_1 conda-forge libiconv 1.17 hd590300_2 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 3.21.12 hfc55251_2 conda-forge libsanitizer 13.2.0 h7e041cc_3 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 13.2.0 ha9c7c90_103 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libthrift 0.18.0 h5e4af38_0 conda-forge libtiff 4.5.0 h6adf6a1_2 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.44.2 hd590300_1 conda-forge libwebp 1.3.2 h11a3e52_0 defaults libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libzlib 1.2.13 hd590300_5 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge ltr_finder 1.07 h4ac6f70_3 bioconda ltr_retriever 2.9.9 hdfd78af_0 bioconda lz4 4.3.3 py39h79d96da_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge mafft 7.520 h031d066_3 bioconda make 4.3 hd18ef5c_1 conda-forge markdown 3.5.2 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py39hd1e30aa_1 conda-forge matplotlib-base 3.8.2 py39he9076e7_0 conda-forge mdust 2006.10.17 h031d066_6 bioconda minimap2 2.26 he4a0461_2 bioconda mpfr 4.2.1 h9458935_0 conda-forge msgpack-python 1.0.7 py39h7633fee_0 conda-forge multidict 6.0.4 py39hd1e30aa_1 conda-forge multiprocess 0.70.15 py39hd1e30aa_1 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge muscle 5.1 h4ac6f70_3 bioconda ncurses 6.4 h59595ed_2 conda-forge nodejs 18.15.0 h8d033a5_0 conda-forge nseg 1.0.1 h031d066_4 bioconda numpy 1.26.3 py39h474f0d3_0 conda-forge oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge openjdk 17.0.3 h58dac75_5 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openssl 3.2.0 hd590300_1 conda-forge opt_einsum 3.3.0 pyhc1e730c_2 conda-forge orc 1.8.2 hfdbbad2_2 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.2.0 py39hddac248_0 conda-forge pango 1.50.14 hd33c08f_0 conda-forge parquet-cpp 1.5.1 2 conda-forge partd 1.4.1 pyhd8ed1ab_0 conda-forge pbzip2 1.1.13 h1fcc475_2 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-app-cpanminus 1.7044 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda perl-constant 1.33 pl526_1 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-gd 2.68 pl526he941832_0 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-text-soundex 3.05 pl526_1000 conda-forge perl-types-serialiser 1.0 pl526_2 bioconda perl-xsloader 0.24 pl526_0 bioconda pigz 2.8 h2797004_0 conda-forge pillow 9.4.0 py39h2320bf1_1 conda-forge pip 23.3.2 pyhd8ed1ab_0 conda-forge pixman 0.43.0 h59595ed_0 conda-forge pp 1.6.4.4 py_0 bioconda protobuf 4.21.12 py39h227be39_0 conda-forge psutil 5.9.8 py39hd1e30aa_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyarrow 11.0.0 py39hf0ef2fd_5_cpu conda-forge pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.9.18 h0755675_1_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-flatbuffers 23.5.26 pyhd8ed1ab_0 conda-forge python-isal 1.5.3 py39hd1e30aa_0 conda-forge python-tzdata 2023.4 pyhd8ed1ab_0 conda-forge python_abi 3.9 4_cp39 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py39hd1e30aa_1 conda-forge r-base 4.2.3 ha7d60f8_0 conda-forge r-cli 3.6.2 r42ha503ecb_0 conda-forge r-colorspace 2.1_0 r42h57805ef_1 conda-forge r-crayon 1.5.2 r42hc72bb7e_2 conda-forge r-dplyr 1.1.4 r42ha503ecb_0 conda-forge r-ellipsis 0.3.2 r42h57805ef_2 conda-forge r-fansi 1.0.6 r42h57805ef_0 conda-forge r-farver 2.1.1 r42ha503ecb_2 conda-forge r-generics 0.1.3 r42hc72bb7e_2 conda-forge r-ggplot2 3.4.4 r42hc72bb7e_0 conda-forge r-glue 1.7.0 r42h57805ef_0 conda-forge r-gtable 0.3.4 r42hc72bb7e_0 conda-forge r-here 1.0.1 r42hc72bb7e_2 conda-forge r-isoband 0.2.7 r42ha503ecb_2 conda-forge r-labeling 0.4.3 r42hc72bb7e_0 conda-forge r-lattice 0.22_5 r42h57805ef_0 conda-forge r-lifecycle 1.0.4 r42hc72bb7e_0 conda-forge r-magrittr 2.0.3 r42h57805ef_2 conda-forge r-mass 7.3_60.0.1 r42h57805ef_0 conda-forge r-matrix 1.6_5 r42h316c678_0 conda-forge r-mgcv 1.9_1 r42h316c678_0 conda-forge r-munsell 0.5.0 r42hc72bb7e_1006 conda-forge r-nlme 3.1_164 r42h61816a4_0 conda-forge r-pillar 1.9.0 r42hc72bb7e_1 conda-forge r-pkgconfig 2.0.3 r42hc72bb7e_3 conda-forge r-purrr 1.0.2 r42h57805ef_0 conda-forge r-r6 2.5.1 r42hc72bb7e_2 conda-forge r-rcolorbrewer 1.1_3 r42h785f33e_2 conda-forge r-rlang 1.1.3 r42ha503ecb_0 conda-forge r-rprojroot 2.0.4 r42hc72bb7e_0 conda-forge r-scales 1.3.0 r42hc72bb7e_0 conda-forge r-stringi 1.7.12 r42h1ae9187_0 conda-forge r-stringr 1.5.1 r42h785f33e_0 conda-forge r-tibble 3.2.1 r42h57805ef_2 conda-forge r-tidyr 1.3.0 r42ha503ecb_1 conda-forge r-tidyselect 1.2.0 r42hc72bb7e_1 conda-forge r-utf8 1.2.4 r42h57805ef_0 conda-forge r-vctrs 0.6.5 r42ha503ecb_0 conda-forge r-viridislite 0.4.2 r42hc72bb7e_1 conda-forge r-withr 3.0.0 r42hc72bb7e_0 conda-forge re2 2023.02.01 hcb278e6_0 conda-forge readline 8.2 h8228510_1 conda-forge recon 1.08 h031d066_6 bioconda regex 2023.12.25 py39hd1e30aa_0 conda-forge repeatmasker 4.1.2.p1 pl5262hdfd78af_0 bioconda repeatmodeler 2.0.1 pl526_0 bioconda repeatscout 1.0.6 hec16e2b_3 bioconda requests 2.31.0 pyhd8ed1ab_0 conda-forge requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge rmblast 2.14.1 h4565617_0 bioconda rsa 4.9 pyhd8ed1ab_0 conda-forge s2n 1.3.37 h3358134_0 conda-forge scikit-learn 1.4.0 py39ha22ef79_0 conda-forge scipy 1.11.4 py39h474f0d3_0 conda-forge sed 4.8 he412f7d_0 conda-forge seqtk 1.4 he4a0461_1 bioconda setuptools 69.0.3 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge swifter 1.4.0 pyhd8ed1ab_0 conda-forge sysroot_linux-64 2.12 he073ed8_16 conda-forge tblib 3.0.0 pyhd8ed1ab_0 conda-forge tensorboard 2.11.2 pyhd8ed1ab_0 conda-forge tensorboard-data-server 0.6.1 py39h3ccb8fc_4 conda-forge tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge tensorflow 2.11.0 cpu_py39h4655687_0 conda-forge tensorflow-base 2.11.0 cpu_py39h9b4020c_0 conda-forge tensorflow-cpu 2.11.0 cpu_py39h718b53a_0 conda-forge tensorflow-estimator 2.11.0 cpu_py39hf050123_0 conda-forge termcolor 2.4.0 pyhd8ed1ab_0 conda-forge tesorter 1.4.6 pyhdfd78af_0 bioconda threadpoolctl 3.2.0 pyha21a80b_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tktable 2.10 h0c5db8f_5 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.3.3 py39hd1e30aa_1 conda-forge tqdm 4.66.1 pyhd8ed1ab_0 conda-forge trf 4.09.1 h031d066_4 bioconda typing-extensions 4.9.0 hd8ed1ab_0 conda-forge typing_extensions 4.9.0 pyha770c72_0 conda-forge tzdata 2023d h0c530f3_0 conda-forge unicodedata2 15.1.0 py39hd1e30aa_0 conda-forge urllib3 2.1.0 pyhd8ed1ab_0 conda-forge werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha35d2d1_1 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge wrapt 1.16.0 py39hd1e30aa_0 conda-forge xopen 1.8.0 py39hf3d152e_0 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.3.0 hd590300_0 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xyzservices 2023.10.1 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.9.4 py39hd1e30aa_0 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstandard 0.22.0 py39h6e5214e_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge
Then run "test" with the following script"
cd /home/lcb/edta-master/test
perl /home/lcb/edta-master/EDTA.pl --genome genome.fa
--cds genome.cds.fa
--curatedlib ../database/rice7.0.0.liban
--exclude genome.exclude.bed
--overwrite 1 --sensitive 1 --anno 1 --threads 10
2> edta.pl.log
Eventually the following error was reported:
2024年 08月 05日 星期一 07:09:14 CST EDTA_raw: Check dependencies, prepare working directories. 2024年 08月 05日 星期一 07:09:14 CST Start to find LTR candidates. 2024年 08月 05日 星期一 07:09:14 CST Identify LTR retrotransposon candidates from scratch. Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. 2024年 08月 05日 星期一 07:09:29 CST Finish finding LTR candidates. 2024年 08月 05日 星期一 07:09:29 CST Start to find SINE candidates. 2024年 08月 05日 星期一 07:10:01 CST Warning: The SINE result file has 0 bp! 2024年 08月 05日 星期一 07:10:01 CST Start to find LINE candidates. 2024年 08月 05日 星期一 07:10:01 CST Identify LINE retrotransposon candidates from scratch. 2024年 08月 05日 星期一 07:10:56 CST Warning: The LINE result file has 0 bp! 2024年 08月 05日 星期一 07:10:56 CST Start to find TIR candidates. 2024年 08月 05日 星期一 07:10:56 CST Identify TIR candidates from scratch. Species: others 2024年 08月 05日 星期一 07:11:16 CST Finish finding TIR candidates. 2024年 08月 05日 星期一 07:11:16 CST Start to find Helitron candidates. 2024年 08月 05日 星期一 07:11:16 CST Identify Helitron candidates from scratch. 2024年 08月 05日 星期一 07:11:40 CST Finish finding Helitron candidates. 2024年 08月 05日 星期一 07:11:40 CST Execution of EDTA_raw.pl is finished! Warning: No sequences were masked 2024年 08月 05日 星期一 07:12:03 CST Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch. Error encountered: [Errno 2] No such file or directory: 'bedtools' mv: 对 'chromosome_density_plots.pdf' 调用 stat 失败: 没有那个文件或目录 Use of uninitialized value $mod_time in localtime at /home/lcb/edta-master/EDTA.pl line 847. cp: 对 'genome.fa.mod.EDTA.TEanno.density_plots.pdf' 调用 stat 失败: 没有那个文件或目录
Does this affect the ./test/genome.fa.mod.EDTA.final/genome.fa.mod.EDTA.TElib.fa files? If it has an effect, how should I fix this reported error? Thank you!
Hi liangchengbo, currently I recommend using
git clone https://github.com/oushujun/EDTA.git
and
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner
to install. This is list of updated dependencies and includes bedtools. Let me know if you succeed.
Faye
Thanks for the suggestion,Faye. But there are some new error reported.
2024年 08月 08日 星期四 17:47:21 CST EDTA_raw: Check dependencies, prepare working directories.
2024年 08月 08日 星期四 17:47:21 CST Start to find LTR candidates.
2024年 08月 08日 星期四 17:47:21 CST Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. 2024年 08月 08日 星期四 17:47:45 CST Finish finding LTR candidates.
2024年 08月 08日 星期四 17:47:45 CST Start to find SINE candidates.
2024年 08月 08日 星期四 17:48:16 CST Warning: The SINE result file has 0 bp!
2024年 08月 08日 星期四 17:48:16 CST Start to find LINE candidates.
2024年 08月 08日 星期四 17:48:16 CST Identify LINE retrotransposon candidates from scratch.
2024年 08月 08日 星期四 17:49:42 CST Warning: The LINE result file has 0 bp!
2024年 08月 08日 星期四 17:49:42 CST Start to find TIR candidates.
2024年 08月 08日 星期四 17:49:42 CST Identify TIR candidates from scratch.
Species: others
Traceback (most recent call last):
File "/home/lcb/edta-master/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in
2024年 08月 08日 星期四 17:49:45 CST Start to find Helitron candidates.
2024年 08月 08日 星期四 17:49:45 CST Identify Helitron candidates from scratch.
2024年 08月 08日 星期四 17:50:08 CST Finish finding Helitron candidates.
2024年 08月 08日 星期四 17:50:08 CST Execution of EDTA_raw.pl is finished!
Warning: No sequences were masked 2024年 08月 08日 星期四 17:50:33 CST Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch.
mv: 对 'chromosome_density_plots.pdf' 调用 stat 失败: 没有那个文件或目录 Use of uninitialized value $mod_time in localtime at /home/lcb/edta-master/EDTA.pl line 847. cp: 对 'genome.fa.mod.EDTA.TEanno.density_plots.pdf' 调用 stat 失败: 没有那个文件或目录
@FayeFang17 Hello, I meet the same issue when I run test file.
I install EDTA by:
- git clone https://github.com/oushujun/EDTA.git
- mamba env create -f EDTA_2.2.x.yml
the log file shows:
Sun Aug 11 14:49:25 CST 2024 Perform post-EDTA analysis for whole-genome annotation:
Sun Aug 11 14:49:25 CST 2024 Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch.
mv: cannot stat 'chromosome_density_plots.pdf': No such file or directory
Sun Aug 11 14:50:08 CST 2024 TE annotation using the EDTA library has finished! Check out:
Whole-genome TE annotation (total TE: 34.61%): genome.fa.mod.EDTA.TEanno.gff3
Whole-genome TE annotation summary: genome.fa.mod.EDTA.TEanno.sum
Whole-genome TE divergence plot: genome.fa.mod_divergence_plot.pdf
Whole-genome TE density plot: genome.fa.mod.EDTA.TEanno.density_plots.pdf
Low-threshold TE masking for MAKER gene annotation (masked: 17.27%): genome.fa.mod.MAKER.masked
Use of uninitialized value $mod_time in localtime at ../EDTA.pl line 847.
cp: cannot stat 'genome.fa.mod.EDTA.TEanno.density_plots.pdf': No such file or directory
Sun Aug 11 14:50:09 CST 2024 Evaluate the level of inconsistency for whole-genome TE annotation:
I downloaded and installed EDTA the same way I did initially. after getting into the EDTA environment, I downloaded and installed bedtools.
mamba install bedtools
And then I copied the installed bedtools to the share folder of the EDTA environment.
Since then, I've run my own data without the above errors. However, it still reports errors when running test data. I'm guessing it's a test data issue.
@FayeFang17 Following issue:
install still have issues with the TIR
mamba install -y -c bioconda -c conda-forge -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner
git clone https://github.com/oushujun/EDTA.git
test:
perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --threads 10
errors:
Species: others
Traceback (most recent call last):
File "/ebio/abt6/zbao/software/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in <module>
from bin.main import TIRLearner
ModuleNotFoundError: No module named 'bin.main'
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /ebio/abt6/zbao/software/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
Author: Shujun Ou ([email protected]) 10/11/2019
mv: cannot stat 'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'genome.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
ERROR: No such file or directory at /ebio/abt6/zbao/software/EDTA/util/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.TIR.intact.raw.fa
If you believe the program is working properly, this may be caused by the lack of intact TIRs in your genome. Consider to use the --force 1 parameter to overwrite this check
To install the released version (master branch), please use:
mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter
if you wish to try out the EDTA2 branch that is under active development, please use:
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner
For the EDTA2 branch, it's better to install fresh because we updated the TIR-Learner recipe recently, and may be in conflict with previous dependencies. After git clone the lastest EDTA repo, you will need to manually switch to the EDTA2 branch:
git checkout EDTA2
Let us know if you have further issues! Shujun
Hi Shujun, thank you for developing this great software for TE annotation I can successfully run the test data from the EDTA installation below
git clone -b master https://github.com/oushujun/EDTA.git
and I added bedtools and samtools for your recommended coomands (because it raised error without samtools and bedtools for panEDTA.sh)
mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter samtools bedtools
However, when I tried it on my own individual genome (~800MB), it gave the following error. Please help me, as I’m planning to quickly do a panTE project from EDTA.
perl ../EDTA_raw.pl --genome AE.fa --type tir --overwrite 1 --threads 10
Sun Aug 18 15:12:01 CST 2024 EDTA_raw: Check dependencies, prepare working directories.
Sun Aug 18 15:12:29 CST 2024 Start to find TIR candidates.
Sun Aug 18 15:12:29 CST 2024 Identify TIR candidates from scratch.
Species: others
/work/home/softwares/miniconda3/envs/EDTA/bin/gt tirvish: error: fopen(): cannot open file 'TIR-Learner-+-gt_index.prj': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /work/home/softwares/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list AE.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
Author: Shujun Ou ([email protected]) 10/11/2019
mv: cannot stat 'AE.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'AE.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'AE.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
ERROR: No such file or directory at /work/home/softwares/EDTA/util/output_by_list.pl line 39.
Error: TIR results not found!
Thanks for the suggestion,Faye. But there are some new error reported.
2024年 08月 08日 星期四 17:47:21 CST EDTA_raw: Check dependencies, prepare working directories.
2024年 08月 08日 星期四 17:47:21 CST Start to find LTR candidates.
2024年 08月 08日 星期四 17:47:21 CST Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. 2024年 08月 08日 星期四 17:47:45 CST Finish finding LTR candidates.
2024年 08月 08日 星期四 17:47:45 CST Start to find SINE candidates.
2024年 08月 08日 星期四 17:48:16 CST Warning: The SINE result file has 0 bp!
2024年 08月 08日 星期四 17:48:16 CST Start to find LINE candidates.
2024年 08月 08日 星期四 17:48:16 CST Identify LINE retrotransposon candidates from scratch.
2024年 08月 08日 星期四 17:49:42 CST Warning: The LINE result file has 0 bp!
2024年 08月 08日 星期四 17:49:42 CST Start to find TIR candidates.
2024年 08月 08日 星期四 17:49:42 CST Identify TIR candidates from scratch.
Species: others Traceback (most recent call last): File "/home/lcb/edta-master/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in from bin.main import TIRLearner File "/home/lcb/edta-master/bin/TIR-Learner3.0/bin/main.py", line 22, in from prog_const import * File "/home/lcb/edta-master/bin/TIR-Learner3.0/bin/prog_const.py", line 29, in import tensorflow as tf ModuleNotFoundError: No module named 'tensorflow' 2024年 08月 08日 星期四 17:49:45 CST Finish finding TIR candidates.
2024年 08月 08日 星期四 17:49:45 CST Start to find Helitron candidates.
2024年 08月 08日 星期四 17:49:45 CST Identify Helitron candidates from scratch.
2024年 08月 08日 星期四 17:50:08 CST Finish finding Helitron candidates.
2024年 08月 08日 星期四 17:50:08 CST Execution of EDTA_raw.pl is finished!
Warning: No sequences were masked 2024年 08月 08日 星期四 17:50:33 CST Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch.
mv: 对 'chromosome_density_plots.pdf' 调用 stat 失败: 没有那个文件或目录 Use of uninitialized value $mod_time in localtime at /home/lcb/edta-master/EDTA.pl line 847. cp: 对 'genome.fa.mod.EDTA.TEanno.density_plots.pdf' 调用 stat 失败: 没有那个文件或目录
I have encountered the same problem, I don't know whether directly installing tensorflow package can solve it, I hope there is a good solution to adapt to this version. @oushujun
Error reported when I installed tensorflow directly.
Species: others
/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/bin/process_de_novo_result.py:33: SyntaxWarning: invalid escape sequence '\d'
pattern = '(\d+)'
Traceback (most recent call last):
File "/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 80, in <module>
TIRLearner_instance = TIRLearner(genome_file, genome_name, species, TIR_length,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/bin/main.py", line 81, in __init__
self.execute()
File "/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/bin/main.py", line 121, in execute
self.execute_M4()
File "/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/bin/main.py", line 672, in execute_M4
self["base"] = CNN_predict.execute(self)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 114, in execute
df = predict(df, TIRLearner_instance.genome_file_path,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 62, in predict
model = load_model(path_to_model)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/jwli1/micromamba/envs/EDTA2.2/lib/python3.12/site-packages/keras/src/saving/saving_api.py", line 204, in load_model
raise ValueError(
ValueError: File format not supported: filepath=/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/cnn0912_tf_savedmodel. Keras 3 only supports V3 `.keras` files and legacy H5 format files (`.h5` extension). Note that the legacy SavedModel format is not supported by `load_model()` in Keras 3. In order to reload a TensorFlow SavedModel as an inference-only layer in Keras 3, use `keras.layers.TFSMLayer(/public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/bin/TIR-Learner3.0/cnn0912_tf_savedmodel, call_endpoint='serving_default')` (note that your `call_endpoint` might have a different name).
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
Author: Shujun Ou ([email protected]) 10/11/2019
mv: cannot stat 'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'genome.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
ERROR: No such file or directory at /public/home/jwli1/data1/Brasscia_2024/02.TE/EDTA2/EDTA/util/output_by_list.pl line 39.
Error: TIR results not found!
ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.TIR.intact.raw.fa
If you believe the program is working properly, this may be caused by the lack of intact TIRs in your genome. Consider to use the --force 1 parameter to overwrite this check
To install the released version (master branch), please use:
mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorterif you wish to try out the EDTA2 branch that is under active development, please use:
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScannerFor the EDTA2 branch, it's better to install fresh because we updated the TIR-Learner recipe recently, and may be in conflict with previous dependencies. After git clone the lastest EDTA repo, you will need to manually switch to the EDTA2 branch:
git checkout EDTA2Let us know if you have further issues! Shujun
Dear Ou, Following your suggestion, i git clone EDTA (git clone https://github.com/oushujun/EDTA.git) and install dependences by mamba : mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter
But when i run the test command, there still are some warnnings, such as: Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Warning: The SINE result file has 0 bp! Warning: The LINE result file has 0 bp! Warning: No sequences were masked
and the result in genome.fa.mod.EDTA.TEanno.sum is : Repeat Classes
Total Sequences: 1
Total Length: 1000000 bp
Class Count bpMasked %masked
===== ===== ======== =======
LINE -- -- --
unknown 39 13979 1.40%
LTR -- -- --
Copia 11 18647 1.86%
Gypsy 48 108654 10.87%
TRIM 1 129 0.01%
unknown 1 248 0.02%
SINE -- -- --
unknown 11 1775 0.18%
TIR -- -- --
CACTA 23 22722 2.27%
Mutator 115 47072 4.71%
PIF_Harbinger 110 28045 2.80%
PILE 4 1033 0.10%
POLE 2 506 0.05%
Tc1_Mariner 124 48718 4.87%
hAT 35 13953 1.40%
unknown 9 1433 0.14%
nonTIR -- -- --
helitron 56 39164 3.92%
---------------------------------
total interspersed 589 346078 34.61%
Total 589 346078 34.61%
It looks like that the EDTA has finished successfully. Is it ok with above warnnings? And can i use the result "genome.fa.mod.EDTA.TElib.fa" for further TE mask of RepeatMasker? Is it complete result or broken result?
Thank you very much!!!
To install the released version (master branch), please use:
mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorterif you wish to try out the EDTA2 branch that is under active development, please use:mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScannerFor the EDTA2 branch, it's better to install fresh because we updated the TIR-Learner recipe recently, and may be in conflict with previous dependencies. After git clone the lastest EDTA repo, you will need to manually switch to the EDTA2 branch:git checkout EDTA2Let us know if you have further issues! ShujunDear Ou, Following your suggestion, i git clone EDTA (git clone https://github.com/oushujun/EDTA.git) and install dependences by mamba : mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter
But when i run the test command, there still are some warnnings, such as: Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Warning: The SINE result file has 0 bp! Warning: The LINE result file has 0 bp! Warning: No sequences were masked
and the result in genome.fa.mod.EDTA.TEanno.sum is :
Repeat Classes Total Sequences: 1 Total Length: 1000000 bp Class Count bpMasked %masked ===== ===== ======== ======= LINE -- -- -- unknown 39 13979 1.40% LTR -- -- -- Copia 11 18647 1.86% Gypsy 48 108654 10.87% TRIM 1 129 0.01% unknown 1 248 0.02% SINE -- -- -- unknown 11 1775 0.18% TIR -- -- -- CACTA 23 22722 2.27% Mutator 115 47072 4.71% PIF_Harbinger 110 28045 2.80% PILE 4 1033 0.10% POLE 2 506 0.05% Tc1_Mariner 124 48718 4.87% hAT 35 13953 1.40% unknown 9 1433 0.14% nonTIR -- -- -- helitron 56 39164 3.92% --------------------------------- total interspersed 589 346078 34.61%
Total 589 346078 34.61%
It looks like that the EDTA has finished successfully. Is it ok with above warnnings? And can i use the result "genome.fa.mod.EDTA.TElib.fa" for further TE mask of RepeatMasker? Is it complete result or broken result?
Thank you very much!!!
hi ，I met the same issue ，Did you solve it ？Is it ok with the result？thanks.
Bad news: I did not solve this problem. And thouth there is no error when running "test", there also 1occured some errors when i am running my own data. So i finally gave up using this software.
-----原始邮件----- 发件人:huaixiaolu @.> 发送时间:2024-09-27 16:02:55 (星期五) 收件人: oushujun/EDTA @.> 抄送: lly1214 @.>, Comment @.> 主题: Re: [oushujun/EDTA] An error when running ‘test’, probably related to 'bedtools' (Issue #489)
To install the released version (master branch), please use: mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter if you wish to try out the EDTA2 branch that is under active development, please use: mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner For the EDTA2 branch, it's better to install fresh because we updated the TIR-Learner recipe recently, and may be in conflict with previous dependencies. After git clone the lastest EDTA repo, you will need to manually switch to the EDTA2 branch: git checkout EDTA2 Let us know if you have further issues! Shujun
Dear Ou, Following your suggestion, i git clone EDTA (git clone https://github.com/oushujun/EDTA.git) and install dependences by mamba : mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter
But when i run the test command, there still are some warnnings, such as: Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Warning: The SINE result file has 0 bp! Warning: The LINE result file has 0 bp! Warning: No sequences were masked
and the result in genome.fa.mod.EDTA.TEanno.sum is :
Repeat Classes Total Sequences: 1 Total Length: 1000000 bp Class Count bpMasked %masked ===== ===== ======== ======= LINE -- -- -- unknown 39 13979 1.40% LTR -- -- -- Copia 11 18647 1.86% Gypsy 48 108654 10.87% TRIM 1 129 0.01% unknown 1 248 0.02% SINE -- -- -- unknown 11 1775 0.18% TIR -- -- -- CACTA 23 22722 2.27% Mutator 115 47072 4.71% PIF_Harbinger 110 28045 2.80% PILE 4 1033 0.10% POLE 2 506 0.05% Tc1_Mariner 124 48718 4.87% hAT 35 13953 1.40% unknown 9 1433 0.14% nonTIR -- -- -- helitron 56 39164 3.92% --------------------------------- total interspersed 589 346078 34.61%
Total 589 346078 34.61%
It looks like that the EDTA has finished successfully. Is it ok with above warnnings? And can i use the result "genome.fa.mod.EDTA.TElib.fa" for further TE mask of RepeatMasker? Is it complete result or broken result?
Thank you very much!!!
hi ，I met the same issue ，Did you solve it ？Is it ok with the result？thanks.
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>
Bad news: I did not solve this problem. And thouth there is no error when running "test", there also 1occured some errors when i am running my own data. So i finally gave up using this software. … -----原始邮件----- 发件人:huaixiaolu @.> 发送时间:2024-09-27 16:02:55 (星期五) 收件人: oushujun/EDTA @.> 抄送: lly1214 @.>, Comment @.> 主题: Re: [oushujun/EDTA] An error when running ‘test’, probably related to 'bedtools' (Issue #489) To install the released version (master branch), please use: mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter if you wish to try out the EDTA2 branch that is under active development, please use: mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner For the EDTA2 branch, it's better to install fresh because we updated the TIR-Learner recipe recently, and may be in conflict with previous dependencies. After git clone the lastest EDTA repo, you will need to manually switch to the EDTA2 branch: git checkout EDTA2 Let us know if you have further issues! Shujun Dear Ou, Following your suggestion, i git clone EDTA (git clone https://github.com/oushujun/EDTA.git) and install dependences by mamba : mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter But when i run the test command, there still are some warnnings, such as: Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Warning: The SINE result file has 0 bp! Warning: The LINE result file has 0 bp! Warning: No sequences were masked and the result in genome.fa.mod.EDTA.TEanno.sum is : Repeat Classes Total Sequences: 1 Total Length: 1000000 bp Class Count bpMasked %masked ===== ===== ======== ======= LINE -- -- -- unknown 39 13979 1.40% LTR -- -- -- Copia 11 18647 1.86% Gypsy 48 108654 10.87% TRIM 1 129 0.01% unknown 1 248 0.02% SINE -- -- -- unknown 11 1775 0.18% TIR -- -- -- CACTA 23 22722 2.27% Mutator 115 47072 4.71% PIF_Harbinger 110 28045 2.80% PILE 4 1033 0.10% POLE 2 506 0.05% Tc1_Mariner 124 48718 4.87% hAT 35 13953 1.40% unknown 9 1433 0.14% nonTIR -- -- -- helitron 56 39164 3.92% --------------------------------- total interspersed 589 346078 34.61% Total 589 346078 34.61% It looks like that the EDTA has finished successfully. Is it ok with above warnnings? And can i use the result "genome.fa.mod.EDTA.TElib.fa" for further TE mask of RepeatMasker? Is it complete result or broken result? Thank you very much!!! hi ，I met the same issue ，Did you solve it ？Is it ok with the result？thanks. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>
I have the same issue. I have tried various methods to install panEDTA, but it's still not working for real data.
@oushujun , could you help us resolve this issue so we can start using panEDTA as soon as possible. Since we have used EDTA before with good results and are familiar with it, we prefer to use it for analyzing panTE. Thanks.
Hello,
Sorry for the delay. Warnings in the test run is fine. This thread is not about panEDTA. Please create a new thread with your error messages.
Thanks, Shujun
On Fri, Sep 27, 2024 at 7:58 AM Lin Cheng @.***> wrote:
Bad news: I did not solve this problem. And thouth there is no error when running "test", there also 1occured some errors when i am running my own data. So i finally gave up using this software. … <#m_4099005838265658474_> -----原始邮件----- 发件人:huaixiaolu @.> 发送时间:2024-09-27 16:02:55 (星期五) 收件人: oushujun/EDTA @.> 抄送: lly1214 @.>, Comment @.> 主题: Re: [oushujun/EDTA] An error when running ‘test’, probably related to 'bedtools' (Issue #489 https://github.com/oushujun/EDTA/issues/489) To install the released version (master branch), please use: mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter if you wish to try out the EDTA2 branch that is under active development, please use: mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner For the EDTA2 branch, it's better to install fresh because we updated the TIR-Learner recipe recently, and may be in conflict with previous dependencies. After git clone the lastest EDTA repo, you will need to manually switch to the EDTA2 branch: git checkout EDTA2 Let us know if you have further issues! Shujun Dear Ou, Following your suggestion, i git clone EDTA (git clone https://github.com/oushujun/EDTA.git) and install dependences by mamba : mamba create -n EDTA -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter But when i run the test command, there still are some warnnings, such as: Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Warning: The SINE result file has 0 bp! Warning: The LINE result file has 0 bp! Warning: No sequences were masked and the result in genome.fa.mod.EDTA.TEanno.sum is : Repeat Classes Total Sequences: 1 Total Length: 1000000 bp Class Count bpMasked %masked ===== ===== ======== ======= LINE -- -- -- unknown 39 13979 1.40% LTR -- -- -- Copia 11 18647 1.86% Gypsy 48 108654 10.87% TRIM 1 129 0.01% unknown 1 248 0.02% SINE -- -- -- unknown 11 1775 0.18% TIR -- -- -- CACTA 23 22722 2.27% Mutator 115 47072 4.71% PIF_Harbinger 110 28045 2.80% PILE 4 1033 0.10% POLE 2 506 0.05% Tc1_Mariner 124 48718 4.87% hAT 35 13953 1.40% unknown 9 1433 0.14% nonTIR -- -- -- helitron 56 39164 3.92% --------------------------------- total interspersed 589 346078 34.61% Total 589 346078 34.61% It looks like that the EDTA has finished successfully. Is it ok with above warnnings? And can i use the result "genome.fa.mod.EDTA.TElib.fa" for further TE mask of RepeatMasker? Is it complete result or broken result? Thank you very much!!! hi ，I met the same issue ，Did you solve it ？Is it ok with the result？thanks. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>
I have the same issue. I have tried various methods to install panEDTA, but it's still not working for real data.
@oushujun https://github.com/oushujun , could you help us resolve this issue so we can start using panEDTA as soon as possible. Since we have used EDTA before with good results and are familiar with it, we prefer to use it for analyzing panTE. Thanks.
— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/489#issuecomment-2379106940, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBBYHI3BQ7XNDLLB5LZYVB6DAVCNFSM6AAAAABL76OU6SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZZGEYDMOJUGA . You are receiving this because you were mentioned.Message ID: @.***>
@jwli-code You have error No module named 'tensorflow', this is because you installed the EDTA dependencies but used it to run EDTA2, which relies on different dependencies. Please use matching versions. Check out #497 for more details.
Shujun