How to install EDTA? #497
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Also experiencing since updating to latest commits on master and using conda environment specified in #489 (comment) |
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May I ask how did you install EDTA? |
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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 |
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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: ***@***.***>
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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.
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Hello, The conda recipe has not yet been updated, so please use the following command to install dependencies: For EDTA2 Thanks! |
This was referenced Oct 7, 2024
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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.
This is my log. This is my errlog |
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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
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.3 h5888daf_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-devel_linux-64 14.2.0 h41c2201_101 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgettextpo 0.22.5 he02047a_3 conda-forge
libgettextpo-devel 0.22.5 he02047a_3 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran-ng 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libgoogle-cloud 2.24.0 h2736e30_0 conda-forge
libgoogle-cloud-storage 2.24.0 h3d9a0c8_0 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libidn2 2.3.7 hd590300_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 25_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.28 pthreads_h94d23a6_0 conda-forge
libopenssl-static 3.3.2 hb9d3cd8_0 conda-forge
libparquet 16.1.0 h6a7eafb_6_cpu conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 4.25.3 h08a7969_0 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
libsanitizer 14.2.0 h2a3dede_1 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-devel_linux-64 14.2.0 h41c2201_101 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libthrift 0.19.0 hb90f79a_1 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libtorch 2.4.0 cpu_generic_h4a3044c_1 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 1.48.0 hd590300_0 conda-forge
libwebp 1.4.0 h2c329e2_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 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_finder_parallel 1.1 hdfd78af_1 bioconda
ltr_harvest_parallel 1.1 hdfd78af_1 bioconda
ltr_retriever 3.0.1 hdfd78af_0 bioconda
lz4 4.3.3 py312hb3f7f12_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
make 4.4.1 hb9d3cd8_2 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.2 py312h178313f_0 conda-forge
matplotlib-base 3.9.2 py312hd3ec401_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
mdust 2006.10.17 h031d066_6 bioconda
minimap2 2.28 he4a0461_3 bioconda
ml_dtypes 0.5.0 py312hf9745cd_0 conda-forge
mpc 1.3.1 h24ddda3_1 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.1.0 py312h68727a3_0 conda-forge
multiprocess 0.70.17 py312h66e93f0_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
namex 0.0.8 pyhd8ed1ab_0 conda-forge
ncbi-vdb 3.1.1 h4ac6f70_2 bioconda
ncurses 6.5 he02047a_1 conda-forge
networkx 3.4.2 pyhd8ed1ab_1 conda-forge
ninja-nj 0.98 h4ac6f70_3 bioconda
nodejs 20.12.2 hb753e55_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nseg 1.0.1 h031d066_4 bioconda
numpy 2.1.2 py312h58c1407_0 conda-forge
openjdk 22.0.1 hb622114_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.2 hb9d3cd8_0 conda-forge
optree 0.13.0 py312h68727a3_0 conda-forge
orc 2.0.1 h17fec99_1 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.3 py312hf9745cd_1 conda-forge
pango 1.54.0 h84a9a3c_0 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 10.43 hcad00b1_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 pl5321hbf60520_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321hadc24fc_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 pl5321hb9d3cd8_1 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_3 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 0.242 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 pl5321hb9d3cd8_0 conda-forge
perl-test-fatal 0.016 pl5321ha770c72_0 conda-forge
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 0.31 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 10.3.0 py312hdcec9eb_0 conda-forge
pip 24.3.1 pyh8b19718_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pp 1.6.4.4 py_0 bioconda
psutil 6.1.0 py312h66e93f0_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pyarrow 16.1.0 py312h9cebb41_2 conda-forge
pyarrow-core 16.1.0 py312h0983c49_2_cpu conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.2.0 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.3 hab00c5b_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-isal 1.7.1 py312h66e93f0_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_0 conda-forge
python-zlib-ng 0.5.1 py312h27ca174_0 conda-forge
python_abi 3.12 5_cp312 conda-forge
pytorch 2.4.0 cpu_generic_py312h1576ffb_1 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h66e93f0_1 conda-forge
qhull 2020.2 h434a139_5 conda-forge
r-base 4.4.0 h019f4a6_1 conda-forge
r-cli 3.6.3 r44h0d4f4ea_1 conda-forge
r-colorspace 2.1_1 r44hdb488b9_0 conda-forge
r-crayon 1.5.3 r44hc72bb7e_1 conda-forge
r-dplyr 1.1.4 r44h0d4f4ea_1 conda-forge
r-ellipsis 0.3.2 r44hb1dbf0f_3 conda-forge
r-fansi 1.0.6 r44hb1dbf0f_1 conda-forge
r-farver 2.1.2 r44ha18555a_1 conda-forge
r-generics 0.1.3 r44hc72bb7e_3 conda-forge
r-ggplot2 3.5.1 r44hc72bb7e_1 conda-forge
r-glue 1.8.0 r44h2b5f3a1_0 conda-forge
r-gtable 0.3.6 r44hc72bb7e_0 conda-forge
r-here 1.0.1 r44hc72bb7e_3 conda-forge
r-isoband 0.2.7 r44ha18555a_3 conda-forge
r-labeling 0.4.3 r44hc72bb7e_1 conda-forge
r-lattice 0.22_6 r44hb1dbf0f_1 conda-forge
r-lifecycle 1.0.4 r44hc72bb7e_1 conda-forge
r-magrittr 2.0.3 r44hb1dbf0f_3 conda-forge
r-mass 7.3_60.0.1 r44hb1dbf0f_1 conda-forge
r-matrix 1.6_5 r44he966344_1 conda-forge
r-mgcv 1.9_1 r44h0d28552_1 conda-forge
r-munsell 0.5.1 r44hc72bb7e_1 conda-forge
r-nlme 3.1_165 r44hbcb9c34_1 conda-forge
r-pillar 1.9.0 r44hc72bb7e_2 conda-forge
r-pkgconfig 2.0.3 r44hc72bb7e_4 conda-forge
r-purrr 1.0.2 r44hdb488b9_1 conda-forge
r-r6 2.5.1 r44hc72bb7e_3 conda-forge
r-rcolorbrewer 1.1_3 r44h785f33e_3 conda-forge
r-rlang 1.1.4 r44ha18555a_1 conda-forge
r-rprojroot 2.0.4 r44hc72bb7e_1 conda-forge
r-scales 1.3.0 r44hc72bb7e_1 conda-forge
r-stringi 1.8.4 r44ha8ce623_2 conda-forge
r-stringr 1.5.1 r44h785f33e_1 conda-forge
r-tibble 3.2.1 r44hdb488b9_3 conda-forge
r-tidyr 1.3.1 r44h0d4f4ea_1 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_1 conda-forge
r-utf8 1.2.4 r44hb1dbf0f_1 conda-forge
r-vctrs 0.6.5 r44h0d4f4ea_1 conda-forge
r-viridislite 0.4.2 r44hc72bb7e_2 conda-forge
r-withr 3.0.2 r44hc72bb7e_0 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8228510_1 conda-forge
recon 1.08 h031d066_7 bioconda
regex 2024.9.11 py312h66e93f0_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
rich 13.9.3 pyhd8ed1ab_0 conda-forge
rmblast 2.14.1 h4565617_0 bioconda
rpsbproc 0.5.0 h6a68c12_0 bioconda
s2n 1.4.15 he19d79f_0 conda-forge
samtools 1.21 h50ea8bc_0 bioconda
scikit-learn 1.5.2 py312h7a48858_1 conda-forge
scipy 1.14.1 py312h62794b6_1 conda-forge
sed 4.8 he412f7d_0 conda-forge
seqtk 1.4 he4a0461_2 bioconda
setuptools 75.3.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sleef 3.7 h1b44611_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
swifter 1.4.0 pyhd8ed1ab_0 conda-forge
sympy 1.13.3 pypyh2585a3b_103 conda-forge
sysroot_linux-64 2.17 h4a8ded7_18 conda-forge
tblib 3.0.0 pyhd8ed1ab_0 conda-forge
tesorter 1.4.7 pyhdfd78af_0 bioconda
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tir-learner 3.0.3 hdfd78af_0 bioconda
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h8bc8fbc_6 conda-forge
toolz 1.0.0 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py312h66e93f0_1 conda-forge
tqdm 4.66.6 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 2024b hc8b5060_0 conda-forge
ucsc-fatotwobit 472 he8037a5_0 bioconda
ucsc-twobitinfo 472 h9b8f530_0 bioconda
ucsc-twobittofa 472 h9b8f530_0 bioconda
unicodedata2 15.1.0 py312h66e93f0_1 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
xopen 2.0.2 pyh707e725_1 conda-forge
xorg-fixesproto 5.0 hb9d3cd8_1003 conda-forge
xorg-inputproto 2.3.2 hb9d3cd8_1003 conda-forge
xorg-kbproto 1.0.7 hb9d3cd8_1003 conda-forge
xorg-libice 1.1.1 hb9d3cd8_1 conda-forge
xorg-libsm 1.2.4 he73a12e_1 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hb9d3cd8_1 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_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 h4bc722e_1 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-libxtst 1.2.5 h4bc722e_0 conda-forge
xorg-recordproto 1.14.2 hb9d3cd8_1003 conda-forge
xorg-renderproto 0.11.1 hb9d3cd8_1003 conda-forge
xorg-xextproto 7.3.0 hb9d3cd8_1004 conda-forge
xorg-xproto 7.0.31 hb9d3cd8_1008 conda-forge
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
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The new conda version (v2.2.2, https://anaconda.org/bioconda/edta) should be installed fine now. Unpinning this issue. Shujun |
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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, line 4266. Can this error could be repaired or are there any metohd to deal with this problem?
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