An error when running ‘test’, probably related to 'bedtools' #489
Comments
|
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 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 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 mv: 对 'chromosome_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:
the log file shows: |
|
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 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: if you wish to try out the EDTA2 branch that is under active development, please use: 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: Let us know if you have further issues! |
|
Thanks, now it finish without further errors. |
|
Hi Shujun, thank you for developing this great software for TE annotation
and I added bedtools and samtools for your recommended coomands (because it raised error without samtools and bedtools for panEDTA.sh)
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. |
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. |
Dear Ou, But when i run the test command, there still are some warnnings, such as: and the result in genome.fa.mod.EDTA.TEanno.sum is :
|
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: ***@***.***>
|
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 <#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
<#489 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABNX4NBBYHI3BQ7XNDLLB5LZYVB6DAVCNFSM6AAAAABL76OU6SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZZGEYDMOJUGA>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
@jwli-code You have error Shujun |
|
@lly1214 sorry, what was the error message on your data? Shujun |
|
The v2.2.2 release should fix this issue. It's available on conda. Shujun |
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!
The text was updated successfully, but these errors were encountered: