oushujun
An error in the LTR.identifier.pl
When I run the program EDTA, an error occurred during the initial process: Invalid value for shared scalar at /lustre/home/huli/micromamba/envs/edta/share/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> line 4266. Can this error could be repaired or are there any metohd to deal with this problem?
Also experiencing since updating to latest commits on master and using conda environment specified in https://github.com/oushujun/EDTA/issues/489#issuecomment-2286615602
For me, that was using the conda environment recommended in the comment I linked (the master branch env, not the EDTA2 dev one). I have pasted the resulting environment below. In the end I have opted to use docker://quay.io/biocontainers/edta:2.0.0--hdfd78af_0 which runs fine :) (although which needs to be unset prior to running due to BusyBox)
# 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
_sysroot_linux-64_curr_repodata_hack 3 h69a702a_16 conda-forge
absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
aiohappyeyeballs 2.4.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.10.5 py310h5b4e0ec_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
annosine2 2.0.7 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 24.2.0 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 ha1999f0_7 conda-forge
biopython 1.84 py310hc51659f_0 conda-forge
blast 2.16.0 hc155240_2 bioconda
blinker 1.8.2 pyhd8ed1ab_0 conda-forge
bokeh 3.5.2 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 py310hd8f1fbe_9 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.33.1 heb4867d_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.5.0 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
cd-hit 4.8.1 h43eeafb_10 bioconda
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.17.0 py310h2fdcea3_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 1.2.1 py310hd41b1e2_0 conda-forge
coreutils 9.5 hd590300_0 conda-forge
cryptography 43.0.0 py310h4909e49_0 conda-forge
curl 8.1.2 h409715c_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.3 py310h2372a71_0 conda-forge
dask 2024.8.1 pyhd8ed1ab_0 conda-forge
dask-core 2024.8.1 pyhd8ed1ab_0 conda-forge
dask-expr 1.1.11 pyhd8ed1ab_0 conda-forge
dill 0.3.8 pyhd8ed1ab_0 conda-forge
distributed 2024.8.1 pyhd8ed1ab_0 conda-forge
drmaa 0.7.9 py_1000 conda-forge
entrez-direct 22.4 he881be0_0 bioconda
expat 2.6.2 h59595ed_0 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_2 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 4.53.1 py310h5b4e0ec_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
frozenlist 1.4.1 py310h2372a71_0 conda-forge
fsspec 2024.6.1 pyhff2d567_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
gawk 5.3.0 ha916aea_0 conda-forge
gcc_impl_linux-64 14.1.0 h3c94d91_0 conda-forge
genericrepeatfinder 1.0.2 h4ac6f70_0 bioconda
genometools-genometools 1.6.4 py310h3db02ab_0 bioconda
gettext 0.22.5 he02047a_3 conda-forge
gettext-tools 0.22.5 he02047a_3 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
gfortran_impl_linux-64 14.1.0 he4a1faa_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glob2 0.7 py_0 conda-forge
glog 0.6.0 h6f12383_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
google-auth 2.34.0 pyhff2d567_0 conda-forge
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
google-pasta 0.2.0 pyhd8ed1ab_1 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
grpcio 1.51.1 py310h4a5735c_1 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 14.1.0 h8d00ecb_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.9.0 nompi_py310hcca72df_101 conda-forge
harfbuzz 6.0.0 h8e241bc_0 conda-forge
hdf5 1.14.1 nompi_h4f84152_100 conda-forge
hmmer 3.4 hdbdd923_2 bioconda
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.8 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.4.0 pyha770c72_0 conda-forge
importlib_metadata 8.4.0 hd8ed1ab_0 conda-forge
irf 3.08 hdbdd923_0 bioconda
isa-l 2.31.0 h4bc722e_2 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 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 3.10.0 h4a8ded7_16 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge
krb5 1.20.1 h81ceb04_0 conda-forge
lcms2 2.15 hfd0df8a_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20220623.0 cxx17_h05df665_6 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libarrow 11.0.0 h2ebd325_5_cpu conda-forge
libasprintf 0.22.5 he8f35ee_3 conda-forge
libasprintf-devel 0.22.5 he8f35ee_3 conda-forge
libblas 3.9.0 23_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 23_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcups 2.3.3 h36d4200_3 conda-forge
libcurl 8.1.2 h409715c_0 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 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 14.1.0 h5d3d1c9_100 conda-forge
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgd 2.3.3 h5aea950_4 conda-forge
libgettextpo 0.22.5 he02047a_3 conda-forge
libgettextpo-devel 0.22.5 he02047a_3 conda-forge
libgfortran-ng 14.1.0 h69a702a_0 conda-forge
libgfortran5 14.1.0 hc5f4f2c_0 conda-forge
libglib 2.78.1 hebfc3b9_0 conda-forge
libgomp 14.1.0 h77fa898_0 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 2.3.7 hd590300_0 conda-forge
liblapack 3.9.0 23_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 3.21.12 hfc55251_2 conda-forge
libsanitizer 14.1.0 hcba0ae0_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-devel_linux-64 14.1.0 h5d3d1c9_100 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 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 1.2.4 h1daa5a0_1 conda-forge
libwebp-base 1.2.4 h166bdaf_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 h4ab18f5_6 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 py310h350c4a5_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
make 4.4.1 hb9d3cd8_0 conda-forge
markdown 3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py310h2372a71_0 conda-forge
matplotlib-base 3.9.2 py310hf02ac8c_0 conda-forge
mdust 2006.10.17 h031d066_6 bioconda
minimap2 2.28 he4a0461_2 bioconda
mpfr 4.2.1 h38ae2d0_2 conda-forge
msgpack-python 1.0.8 py310h25c7140_0 conda-forge
multidict 6.0.5 py310h2372a71_0 conda-forge
multiprocess 0.70.16 py310h2372a71_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
muscle 5.1 h4ac6f70_3 bioconda
mysql-connector-c 6.1.11 h659d440_1008 conda-forge
ncbi-vdb 3.1.1 h4ac6f70_1 bioconda
ncurses 6.5 he02047a_1 conda-forge
ninja-nj 0.98 h4ac6f70_3 bioconda
nodejs 18.15.0 h8d033a5_0 conda-forge
nseg 1.0.1 h031d066_4 bioconda
numpy 1.26.4 py310hb13e2d6_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 3.3.1 hb9d3cd8_3 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
orc 1.8.2 hfdbbad2_2 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py310hf9f9076_1 conda-forge
pango 1.50.14 hd33c08f_0 conda-forge
parquet-cpp 1.5.1 2 conda-forge
partd 1.4.2 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 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-base 2.23 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn 3.007 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn-data 20210112.006 pl5321hd8ed1ab_0 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-devel-size 0.83 pl5321h031d066_4 bioconda
perl-digest-hmac 1.04 pl5321hdfd78af_0 bioconda
perl-digest-md5 2.58 pl5321h166bdaf_0 conda-forge
perl-encode 3.21 pl5321hd590300_0 conda-forge
perl-encode-locale 1.05 pl5321hdfd78af_7 bioconda
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-file-listing 6.16 pl5321hdfd78af_0 bioconda
perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge
perl-file-spec 3.48_01 pl5321hdfd78af_2 bioconda
perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge
perl-file-which 1.24 pl5321hd8ed1ab_0 conda-forge
perl-gd 2.76 pl5321h5b5514e_1 bioconda
perl-html-parser 3.81 pl5321h4ac6f70_1 bioconda
perl-html-tagset 3.20 pl5321hdfd78af_4 bioconda
perl-http-cookies 6.10 pl5321hdfd78af_0 bioconda
perl-http-daemon 6.16 pl5321hdfd78af_0 bioconda
perl-http-date 6.06 pl5321hdfd78af_0 bioconda
perl-http-message 6.36 pl5321hdfd78af_0 bioconda
perl-http-negotiate 6.01 pl5321hdfd78af_4 bioconda
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-html 1.004 pl5321hdfd78af_0 bioconda
perl-io-socket-ssl 2.075 pl5321hd8ed1ab_0 conda-forge
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.03 pl5321h4ac6f70_3 bioconda
perl-libwww-perl 6.67 pl5321hdfd78af_0 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 bioconda
perl-mime-base64 3.16 pl5321h166bdaf_0 conda-forge
perl-net-http 6.22 pl5321hdfd78af_0 bioconda
perl-net-ssleay 1.92 pl5321hf14f497_1 conda-forge
perl-ntlm 1.09 pl5321hdfd78af_5 bioconda
perl-parent 0.241 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-socket 2.027 pl5321h031d066_4 bioconda
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-test-fatal 0.016 pl5321hdfd78af_0 bioconda
perl-test-simple 1.302191 pl5321hd8ed1ab_0 conda-forge
perl-test-warnings 0.031 pl5321ha770c72_0 conda-forge
perl-text-soundex 3.05 pl5321hd8ed1ab_1001 conda-forge
perl-time-local 1.35 pl5321hdfd78af_0 bioconda
perl-timedate 2.33 pl5321hdfd78af_2 bioconda
perl-try-tiny 0.32 pl5321ha770c72_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-uri 5.17 pl5321ha770c72_0 conda-forge
perl-url-encode 0.03 pl5321h9ee0642_0 bioconda
perl-www-robotrules 6.02 pl5321hdfd78af_4 bioconda
pigz 2.8 h2797004_0 conda-forge
pillow 9.4.0 py310h023d228_1 conda-forge
pip 24.2 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pp 1.6.4.4 py_0 bioconda
protobuf 4.21.12 py310heca2aa9_0 conda-forge
psutil 6.0.0 py310hc51659f_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyarrow 11.0.0 py310h633f555_5_cpu conda-forge
pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge
pyasn1 0.6.0 pyhd8ed1ab_0 conda-forge
pyasn1-modules 0.4.0 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyjwt 2.9.0 pyhd8ed1ab_1 conda-forge
pyopenssl 24.2.1 pyhd8ed1ab_2 conda-forge
pyparsing 3.1.4 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-flatbuffers 24.3.25 pyh59ac667_0 conda-forge
python-isal 1.7.0 py310h5b4e0ec_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python-zlib-ng 0.5.0 py310h6420a16_0 conda-forge
python_abi 3.10 5_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py310h5b4e0ec_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
r-base 4.2.3 ha7d60f8_0 conda-forge
r-cli 3.6.3 r42ha18555a_0 conda-forge
r-colorspace 2.1_0 r42h57805ef_1 conda-forge
r-crayon 1.5.3 r42hc72bb7e_0 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 2.1.2 r42ha18555a_0 conda-forge
r-generics 0.1.3 r42hc72bb7e_2 conda-forge
r-ggplot2 3.5.1 r42hc72bb7e_0 conda-forge
r-glue 1.7.0 r42h57805ef_0 conda-forge
r-gtable 0.3.5 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_6 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 0.5.1 r42hc72bb7e_0 conda-forge
r-nlme 3.1_165 r42hbcb9c34_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 1.1.4 r42ha18555a_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 1.3.1 r42ha503ecb_0 conda-forge
r-tidyselect 1.2.1 r42hc72bb7e_0 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_7 bioconda
regex 2024.7.24 py310h5b4e0ec_0 conda-forge
repeatmasker 4.1.2.p1 pl5321hdfd78af_1 bioconda
repeatmodeler 2.0.3 pl5321h9ee0642_0 bioconda
repeatscout 1.0.6 hec16e2b_3 bioconda
requests 2.32.3 pyhd8ed1ab_0 conda-forge
requests-oauthlib 2.0.0 pyhd8ed1ab_0 conda-forge
rmblast 2.14.1 h4565617_0 bioconda
rpsbproc 0.5.0 h6a68c12_0 bioconda
rsa 4.9 pyhd8ed1ab_0 conda-forge
s2n 1.3.37 h3358134_0 conda-forge
scikit-learn 1.5.1 py310h146d792_0 conda-forge
scipy 1.14.1 py310ha3fb0e1_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
seqtk 1.4 he4a0461_2 bioconda
setuptools 72.2.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 hdb0a2a9_1 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
swifter 1.4.0 pyhd8ed1ab_0 conda-forge
sysroot_linux-64 2.17 h4a8ded7_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 py310h600f1e7_4 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
tensorflow 2.11.0 cpu_py310hd1aba9c_0 conda-forge
tensorflow-base 2.11.0 cpu_py310hc9b7e7f_0 conda-forge
tensorflow-estimator 2.11.0 cpu_py310hfed9998_0 conda-forge
termcolor 2.4.0 pyhd8ed1ab_0 conda-forge
tesorter 1.4.6 pyhdfd78af_1 bioconda
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h8bc8fbc_6 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py310hc51659f_0 conda-forge
tqdm 4.66.5 pyhd8ed1ab_0 conda-forge
trf 4.09.1 h031d066_5 bioconda
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
ucsc-fatotwobit 455 h2a80c09_1 bioconda
ucsc-twobitinfo 455 h2a80c09_1 bioconda
ucsc-twobittofa 455 h2a80c09_1 bioconda
unicodedata2 15.1.0 py310h2372a71_0 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
werkzeug 3.0.4 pyhd8ed1ab_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py310h2372a71_0 conda-forge
xopen 2.0.2 pyh707e725_1 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 2024.6.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 py310h2372a71_0 conda-forge
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.20.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zlib-ng 2.2.1 he02047a_0 conda-forge
zstandard 0.23.0 py310h64cae3c_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Hi,
Thank you for your reply.
I had installed EDTA using mamba.
At 2024-09-05 10:32:25, "Faye (Ning) Fang" @.***> wrote:
May I ask how did you install EDTA?
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
Hi,
Thank you for your patient reply.
I had tried to intstall EDTA using Singularity. But another error also occurred: FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://quay.io/biocontainers/edta:2.2.0--hdfd78af_1: pinging container registry quay.io: Get "https://quay.io/v2/": dial tcp: lookup quay.io on 10.1.1.1:53: read udp 10.1.1.250:50881->10.1.1.1:53: read: connection refused.
All analyses are run on the server platform, so it was not clear whether the permission was denied or the website could not be connected regularly.
Hello,
The conda recipe has not yet been updated, so please use the following command to install dependencies:
For EDTA:
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
For EDTA2
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
To use EDTA2, you need to switch to the EDTA2 branch on your local version:
cd ~/path-to-EDTA/EDTA
git checkout EDTA2
git branch
Thanks! Shujun
Hello,
The conda recipe has not yet been updated, so please use the following command to install dependencies: For EDTA:
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 tesorterFor EDTA2
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 HelitronScannerTo use EDTA2, you need to switch to the EDTA2 branch on your local version:cd ~/path-to-EDTA/EDTAgit checkout EDTA2git branchThanks! Shujun
The issue of multiple warnings during test data execution. I'm not sure if these warning messages will affect the results. I followed the installation commands and ran the test command.
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
This is my log.
cat EDTA_test.out
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.2 #####
##### Shujun Ou ([email protected]) #####
#########################################################
Parameters: --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
Fri Nov 1 20:12:57 CST 2024 Dependency checking:
All passed!
A custom library ../database/rice7.0.0.liban is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.
A CDS file genome.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.
A BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.
Fri Nov 1 20:12:59 CST 2024 Obtain raw TE libraries using various structure-based programs:
Fri Nov 1 20:16:20 CST 2024 Obtain raw TE libraries finished.
All intact TEs found by EDTA:
genome.fa.mod.EDTA.intact.raw.fa
genome.fa.mod.EDTA.intact.raw.gff3
Fri Nov 1 20:16:20 CST 2024 Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:
Fri Nov 1 20:16:34 CST 2024 EDTA advance filtering finished.
Fri Nov 1 20:16:34 CST 2024 Perform EDTA final steps to generate a non-redundant comprehensive TE library.
Filter RepeatModeler results that are ignored in the raw step.
Fri Nov 1 20:16:38 CST 2024 Clean up TE-related sequences in the CDS file with TEsorter.
Remove CDS-related sequences in the EDTA library.
Remove CDS-related sequences in intact TEs.
Fri Nov 1 20:16:45 CST 2024 Combine the high-quality TE library rice7.0.0.liban with the EDTA library:
Fri Nov 1 20:16:52 CST 2024 EDTA final stage finished! You may check out:
The final EDTA TE library: genome.fa.mod.EDTA.TElib.fa
Family names of intact TEs have been updated by rice7.0.0.liban: genome.fa.mod.EDTA.intact.gff3
Comparing to the provided library, EDTA found these novel TEs: genome.fa.mod.EDTA.TElib.novel.fa
The provided library has been incorporated into the final library: genome.fa.mod.EDTA.TElib.fa
Fri Nov 1 20:16:52 CST 2024 Perform post-EDTA analysis for whole-genome annotation:
Fri Nov 1 20:17:02 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
Fri Nov 1 20:17:02 CST 2024 Evaluate the level of inconsistency for whole-genome TE annotation:
Fri Nov 1 20:17:07 CST 2024 Evaluation of TE annotation finished! Check out these files:
Overall: genome.fa.mod.EDTA.TE.fa.stat.all.sum
Nested: genome.fa.mod.EDTA.TE.fa.stat.nested.sum
Non-nested: genome.fa.mod.EDTA.TE.fa.stat.redun.sum
If you want to learn more about the formatting and information of these files, please visit:
https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A
This is my errlog
Fri Nov 1 20:12:59 CST 2024 EDTA_raw: Check dependencies, prepare working directories.
Fri Nov 1 20:13:10 CST 2024 Start to find LTR candidates.
Fri Nov 1 20:13:11 CST 2024 Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty.
Fri Nov 1 20:13:29 CST 2024 Finish finding LTR candidates.
Fri Nov 1 20:13:29 CST 2024 Start to find SINE candidates.
Fri Nov 1 20:13:56 CST 2024 Warning: The SINE result file has 0 bp!
Fri Nov 1 20:13:56 CST 2024 Start to find LINE candidates.
Fri Nov 1 20:13:56 CST 2024 Identify LINE retrotransposon candidates from scratch.
Fri Nov 1 20:15:15 CST 2024 Warning: The LINE result file has 0 bp!
Fri Nov 1 20:15:15 CST 2024 Start to find TIR candidates.
Fri Nov 1 20:15:15 CST 2024 Identify TIR candidates from scratch.
Species: others
Fri Nov 1 20:15:48 CST 2024 Finish finding TIR candidates.
Fri Nov 1 20:15:48 CST 2024 Start to find Helitron candidates.
Fri Nov 1 20:15:48 CST 2024 Identify Helitron candidates from scratch.
Fri Nov 1 20:16:20 CST 2024 Finish finding Helitron candidates.
Fri Nov 1 20:16:20 CST 2024 Execution of EDTA_raw.pl is finished!
Warning: No sequences were masked
Fri Nov 1 20:16:52 CST 2024 Homology-based annotation of TEs using genome.fa.mod.EDTA.TElib.fa from scratch.
I don’t see anything wrong. The warning is fine.
Best, Shujun
On Sat, Nov 2, 2024 at 4:09 PM Eric Watson @.***> wrote:
I followed these instructions with a fresh miniforge install, but I am still getting the error that others experienced in this thread. For me, it seems to stem from
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
cd ~/path-to-EDTA/EDTA git checkout EDTA2 git branch
I then ran EDTA on the test data:
$ /home/EDTA/EDTA.pl --genome /home/EDTA/test/genome.fa --cds /home/EDTA/test/genome.cds.fa
#########################################################
Extensive de-novo TE Annotator (EDTA) v2.2.2
Shujun Ou @.***)
#########################################################
Parameters: --genome /home/EDTA/test/genome.fa --cds /home/EDTA/test/genome.cds.fa
Sat 02 Nov 2024 07:53:05 PM UTC Dependency checking: All passed!
A CDS file /home/EDTA/test/genome.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.Sat 02 Nov 2024 07:53:06 PM UTC Obtain raw TE libraries using various structure-based programs: Sat 02 Nov 2024 07:53:06 PM UTC EDTA_raw: Check dependencies, prepare working directories.
Sat 02 Nov 2024 07:53:11 PM UTC Start to find LTR candidates.
Sat 02 Nov 2024 07:53:11 PM UTC Identify LTR retrotransposon candidates from scratch.
Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Sat 02 Nov 2024 07:53:30 PM UTC Finish finding LTR candidates.
Sat 02 Nov 2024 07:53:30 PM UTC Start to find SINE candidates.
Sat 02 Nov 2024 07:53:57 PM UTC Warning: The SINE result file has 0 bp!
Sat 02 Nov 2024 07:53:57 PM UTC Start to find LINE candidates.
Sat 02 Nov 2024 07:53:57 PM UTC Identify LINE retrotransposon candidates from scratch.
Sat 02 Nov 2024 07:55:01 PM UTC Warning: The LINE result file has 0 bp!
Sat 02 Nov 2024 07:55:01 PM UTC Start to find TIR candidates.
Sat 02 Nov 2024 07:55:01 PM UTC Identify TIR candidates from scratch.
Species: others Sat 02 Nov 2024 07:55:50 PM UTC Finish finding TIR candidates.
Sat 02 Nov 2024 07:55:50 PM UTC Start to find Helitron candidates.
Sat 02 Nov 2024 07:55:50 PM UTC Identify Helitron candidates from scratch.
Sat 02 Nov 2024 07:56:18 PM UTC Finish finding Helitron candidates.
Sat 02 Nov 2024 07:56:18 PM UTC Execution of EDTA_raw.pl is finished!
Sat 02 Nov 2024 07:56:18 PM UTC Obtain raw TE libraries finished. All intact TEs found by EDTA: genome.fa.mod.EDTA.intact.raw.fa genome.fa.mod.EDTA.intact.raw.gff3
Sat 02 Nov 2024 07:56:18 PM UTC Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:
Warning: No sequences were masked Sat 02 Nov 2024 07:56:25 PM UTC EDTA advance filtering finished.
Sat 02 Nov 2024 07:56:25 PM UTC Perform EDTA final steps to generate a non-redundant comprehensive TE library.
Skipping the RepeatModeler results (--sensitive 0). Run EDTA.pl --step final --sensitive 1 if you want to add RepeatModeler results.Sat 02 Nov 2024 07:56:25 PM UTC Clean up TE-related sequences in the CDS file with TEsorter.
Remove CDS-related sequences in the EDTA library. Remove CDS-related sequences in intact TEs.Sat 02 Nov 2024 07:56:31 PM UTC EDTA final stage finished! You may check out: The final EDTA TE library: genome.fa.mod.EDTA.TElib.fa (EDTA2.2) $
Here is what I have installed in the mamba env:
$ mamba list
packages in environment at /home/miniforge3/envs/EDTA2.2:
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 alsa-lib 1.2.11 hd590300_1 conda-forge annosine2 2.0.7 pyh7cba7a3_0 bioconda aws-c-auth 0.7.22 h96bc93b_2 conda-forge aws-c-cal 0.6.14 h88a6e22_1 conda-forge aws-c-common 0.9.19 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 h83b837d_6 conda-forge aws-c-event-stream 0.4.2 ha47c788_12 conda-forge aws-c-http 0.8.1 h29d6fba_17 conda-forge aws-c-io 0.14.8 h21d4f22_5 conda-forge aws-c-mqtt 0.10.4 h759edc4_4 conda-forge aws-c-s3 0.5.9 h594631b_3 conda-forge aws-c-sdkutils 0.1.16 h83b837d_2 conda-forge aws-checksums 0.1.18 h83b837d_6 conda-forge aws-crt-cpp 0.26.9 he3a8b3b_0 conda-forge aws-sdk-cpp 1.11.329 hba8bd5f_3 conda-forge bedtools 2.31.1 hf5e1c6e_2 bioconda binutils_impl_linux-64 2.43 h4bf12b8_2 conda-forge biopython 1.84 py312h9a8786e_0 conda-forge blast 2.16.0 hc155240_2 bioconda bokeh 3.6.0 pyhd8ed1ab_0 conda-forge brotli 1.1.0 hb9d3cd8_2 conda-forge brotli-bin 1.1.0 hb9d3cd8_2 conda-forge brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge bwidget 1.9.14 ha770c72_1 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 cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge cd-hit 4.8.1 h43eeafb_10 bioconda certifi 2024.8.30 pyhd8ed1ab_0 conda-forge cffi 1.17.1 py312h06ac9bb_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cloudpickle 3.1.0 pyhd8ed1ab_1 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.3.0 py312h68727a3_2 conda-forge coreutils 9.5 hd590300_0 conda-forge curl 8.8.0 he654da7_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cytoolz 1.0.0 py312h66e93f0_1 conda-forge dask 2024.10.0 pyhd8ed1ab_0 conda-forge dask-core 2024.10.0 pyhd8ed1ab_0 conda-forge dask-expr 1.1.16 pyhd8ed1ab_0 conda-forge dill 0.3.9 pyhd8ed1ab_0 conda-forge distributed 2024.10.0 pyhd8ed1ab_0 conda-forge drmaa 0.7.9 py_1000 conda-forge entrez-direct 22.4 he881be0_0 bioconda expat 2.6.3 h5888daf_0 conda-forge filelock 3.16.1 pyhd8ed1ab_0 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_3 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 4.54.1 py312h178313f_1 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge fsspec 2024.10.0 pyhff2d567_0 conda-forge gawk 5.3.1 hcd3d067_0 conda-forge gcc_impl_linux-64 14.2.0 h6b349bd_1 conda-forge genericrepeatfinder 1.0.2 h4ac6f70_0 bioconda genometools-genometools 1.6.5 py312h16aaebc_2 bioconda gettext 0.22.5 he02047a_3 conda-forge gettext-tools 0.22.5 he02047a_3 conda-forge gflags 2.2.2 h5888daf_1005 conda-forge gfortran_impl_linux-64 14.2.0 hc73f493_1 conda-forge giflib 5.2.2 hd590300_0 conda-forge glob2 0.7 py_0 conda-forge glog 0.7.1 hbabe93e_0 conda-forge gmp 6.3.0 hac33072_2 conda-forge gmpy2 2.1.5 py312h7201bc8_2 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gxx_impl_linux-64 14.2.0 h2c03514_1 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.12.1 nompi_py312hedeef09_102 conda-forge harfbuzz 8.5.0 hfac3d4d_0 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge helitronscanner 1.0 hdfd78af_0 bioconda hmmer 3.4 hdbdd923_2 bioconda hpack 4.0.0 pyh9f0ad1d_0 conda-forge htslib 1.21 h5efdd21_0 bioconda hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge importlib-metadata 8.5.0 pyha770c72_0 conda-forge importlib_metadata 8.5.0 hd8ed1ab_0 conda-forge irf 3.08 hdbdd923_0 bioconda isa-l 2.31.0 h4bc722e_2 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge k8 1.2 h6618dc6_3 bioconda keras 3.6.0 pyhd8ed1ab_0 conda-forge kernel-headers_linux-64 3.10.0 he073ed8_18 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.7 py312h68727a3_0 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.43 h712a8e2_2 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20240116.2 cxx17_he02047a_1 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libarrow 16.1.0 hcb6531f_6_cpu conda-forge libarrow-acero 16.1.0 hac33072_6_cpu conda-forge libarrow-dataset 16.1.0 hac33072_6_cpu conda-forge libarrow-substrait 16.1.0 h7e0c224_6_cpu 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 libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge libcblas 3.9.0 25_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.8.0 hca28451_1 conda-forge libdeflate 1.20 hd590300_0 conda-forge 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xyzservices 2024.9.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.20.2 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h4ab18f5_6 conda-forge zlib-ng 2.2.2 h5888daf_0 conda-forge zstandard 0.23.0 py312hef9b889_1 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge (EDTA2.2) $
— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/497#issuecomment-2453114125, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NDAGWDRUCCSVETEYSLZ6UWPXAVCNFSM6AAAAABM7TMI56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJTGEYTIMJSGU . You are receiving this because you modified the open/close state.Message ID: @.***>
The new conda version (v2.2.2, https://anaconda.org/bioconda/edta) should be installed fine now. Unpinning this issue.
Shujun