Xxi-GitHub commented 6 months ago

$ 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 --evaluate 1 --threads 10 > EDTA.test

2024年 04月 29日星期一 16:53:03 CST EDTA_raw: Check dependencies, prepare working directories.

2024年 04月 29日星期一 16:53:04 CST Start to find LTR candidates.

2024年 04月 29日星期一 16:53:04 CST Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /home/xionglab250/mambaforge/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 11. cp: 对 'genome.fa.mod.retriever.scn.adj' 调用 stat 失败: 没有那个文件或目录 awk: 致命错误：无法打开文件“genome.fa.mod.pass.list”进行读取：没有那个文件或目录 Warning: LOC 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 (shujun.ou.1@gmail.com) 10/11/2019

mv: 对 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln' 调用 stat 失败: 没有那个文件或目录 mv: 对 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list' 调用 stat 失败: 没有那个文件或目录 cp: 对 'genome.fa.mod.LTR.intact.raw.fa.anno.list' 调用 stat 失败: 没有那个文件或目录 ERROR: No such file or directory at /home/xionglab250/mambaforge/envs/EDTA/share/EDTA/util/output_by_list.pl line 39.

perl filter_gff3.pl file.gff3 file.list > new.gff3

2024年 04月 29日星期一 16:53:10 CST Warning: The LTR result file has 0 bp!

2024年 04月 29日星期一 16:53:10 CST Start to find SINE candidates.

2024年 04月 29日星期一 16:53:38 CST Warning: The SINE result file has 0 bp!

2024年 04月 29日星期一 16:53:38 CST Start to find LINE candidates.

2024年 04月 29日星期一 16:53:38 CST Identify LINE retrotransposon candidates from scratch.

2024年 04月 29日星期一 16:54:38 CST Warning: The LINE result file has 0 bp!

2024年 04月 29日星期一 16:54:38 CST Start to find TIR candidates.

2024年 04月 29日星期一 16:54:38 CST Identify TIR candidates from scratch.

Species: others 2024年 04月 29日星期一 16:55:02 CST Finish finding TIR candidates.

2024年 04月 29日星期一 16:55:02 CST Start to find Helitron candidates.

2024年 04月 29日星期一 16:55:02 CST Identify Helitron candidates from scratch.

2024年 04月 29日星期一 16:55:22 CST Finish finding Helitron candidates.

2024年 04月 29日星期一 16:55:22 CST Execution of EDTA_raw.pl is finished!

ERROR: Raw LTR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.raw.fa and genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.intact.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check ############################################### Is it work in testdata？Shown lack of LTR，and we got the same error for another species. Thanks !

oushujun commented 6 months ago

Hello,

Please test with test data. You will need to reinstall EDTA if it doesn’t work on the test data.

Shujun

On Mon, Apr 29, 2024 at 5:01 AM Xxi-GitHub @.***> wrote:

$ 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 --evaluate 1 --threads 10 > EDTA.test

2024年 04月 29日星期一 16:53:03 CST EDTA_raw: Check dependencies, prepare working directories.

2024年 04月 29日星期一 16:53:04 CST Start to find LTR candidates.

2024年 04月 29日星期一 16:53:04 CST Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /home/xionglab250/mambaforge/envs/EDTA/share/LTR_retriever/bin/ LTR.identifier.pl line 114, line 11. cp: 对 'genome.fa.mod.retriever.scn.adj' 调用 stat 失败: 没有那个文件或目录 awk: 致命错误：无法打开文件“genome.fa.mod.pass.list”进行读取：没有那个文件或目录 Warning: LOC 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 @.***) 10/11/2019

mv: 对 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln' 调用 stat 失败: 没有那个文件或目录 mv: 对 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list' 调用 stat 失败: 没有那个文件或目录 cp: 对 'genome.fa.mod.LTR.intact.raw.fa.anno.list' 调用 stat 失败: 没有那个文件或目录 ERROR: No such file or directory at /home/xionglab250/mambaforge/envs/EDTA/share/EDTA/util/output_by_list.pl line 39.

perl filter_gff3.pl file.gff3 file.list > new.gff3

2024年 04月 29日星期一 16:53:10 CST Warning: The LTR result file has 0 bp!

2024年 04月 29日星期一 16:53:10 CST Start to find SINE candidates.

2024年 04月 29日星期一 16:53:38 CST Warning: The SINE result file has 0 bp!

2024年 04月 29日星期一 16:53:38 CST Start to find LINE candidates.

2024年 04月 29日星期一 16:53:38 CST Identify LINE retrotransposon candidates from scratch.

2024年 04月 29日星期一 16:54:38 CST Warning: The LINE result file has 0 bp!

2024年 04月 29日星期一 16:54:38 CST Start to find TIR candidates.

2024年 04月 29日星期一 16:54:38 CST Identify TIR candidates from scratch.

Species: others 2024年 04月 29日星期一 16:55:02 CST Finish finding TIR candidates.

2024年 04月 29日星期一 16:55:02 CST Start to find Helitron candidates.

2024年 04月 29日星期一 16:55:02 CST Identify Helitron candidates from scratch.

2024年 04月 29日星期一 16:55:22 CST Finish finding Helitron candidates.

2024年 04月 29日星期一 16:55:22 CST Execution of EDTA_raw.pl is finished!

ERROR: Raw LTR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.raw.fa and genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.intact.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check ############################################### Is it work in testdata？Shown lack of LTR，and we got the same error for another species. Thanks !

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/458, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NC4G5XUBI7WRAWFMLTY7YD7FAVCNFSM6AAAAABG55IOAOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3DQNBYG42TAOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Xxi-GitHub commented 6 months ago

$ 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 --evaluate 1 --threads 40 > EDTA.test 2024年 04月 30日星期二 00:49:45 CST EDTA_raw: Check dependencies, prepare working directories.

2024年 04月 30日星期二 00:49:46 CST Start to find LTR candidates.

2024年 04月 30日星期二 00:49:46 CST Identify LTR retrotransposon candidates from scratch.

Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. 2024年 04月 30日星期二 00:49:59 CST Finish finding LTR candidates.

2024年 04月 30日星期二 00:49:59 CST Start to find SINE candidates.

2024年 04月 30日星期二 00:50:34 CST Warning: The SINE result file has 0 bp!

2024年 04月 30日星期二 00:50:34 CST Start to find LINE candidates.

2024年 04月 30日星期二 00:50:34 CST Identify LINE retrotransposon candidates from scratch.

cp: 无法获取'genome.fa.mod.RM2.raw.fa' 的文件状态(stat): 没有那个文件或目录 2024年 04月 30日星期二 00:50:34 CST Warning: The LINE result file has 0 bp!

2024年 04月 30日星期二 00:50:34 CST Start to find TIR candidates.

2024年 04月 30日星期二 00:50:34 CST Identify TIR candidates from scratch.

Species: others Traceback (most recent call last): File "/home/xionglab250/mambaforge/envs/edta/share/EDTA/bin/TIR-Learner3.0/TIR-Learner3.0.py", line 14, in from bin.main import TIRLearner File "/home/xionglab250/mambaforge/envs/edta/share/EDTA/bin/TIR-Learner3.0/bin/main.py", line 23, in import CNN_predict File "/home/xionglab250/mambaforge/envs/edta/share/EDTA/bin/TIR-Learner3.0/bin/CNN_predict.py", line 16, in import tensorflow as tf File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/init.py", line 41, in from tensorflow.python.tools import module_util as _module_util File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/init.py", line 46, in from tensorflow.python import data File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/init.py", line 25, in from tensorflow.python.data import experimental File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/experimental/init.py", line 96, in from tensorflow.python.data.experimental import service File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/experimental/service/init.py", line 140, in from tensorflow.python.data.experimental.ops.data_service_ops import distribute File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/experimental/ops/data_service_ops.py", line 25, in from tensorflow.python.data.experimental.ops import compression_ops File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/experimental/ops/compression_ops.py", line 20, in from tensorflow.python.data.util import structure File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/util/structure.py", line 26, in from tensorflow.python.data.util import nest File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/data/util/nest.py", line 41, in from tensorflow.python.framework import sparse_tensor as _sparse_tensor File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/framework/sparse_tensor.py", line 29, in from tensorflow.python.framework import constant_op File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/framework/constant_op.py", line 29, in from tensorflow.python.eager import execute File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/eager/execute.py", line 27, in from tensorflow.python.framework import dtypes File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/tensorflow/python/framework/dtypes.py", line 513, in np.object, File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/numpy/init.py", line 324, in getattr raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'object'. np.object was a deprecated alias for the builtin object. To avoid this error in existing code, use object by itself. Doing this will not modify any behavior and is safe. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: 没有那个文件或目录 at /home/xionglab250/mambaforge/envs/edta/share/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 (shujun.ou.1@gmail.com) 10/11/2019

mv: 无法获取'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln' 的文件状态(stat): 没有那个文件或目录 cp: 无法获取'genome.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list' 的文件状态(stat): 没有那个文件或目录 cp: 无法获取'genome.fa.mod.TIR.intact.raw.fa.anno.list' 的文件状态(stat): 没有那个文件或目录 Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: 没有那个文件或目录. ERROR: No such file or directory at /home/xionglab250/mambaforge/envs/edta/share/EDTA/util/output_by_list.pl line 39. Warning: The TIR result file has 0 bp!

2024年 04月 30日星期二 00:50:36 CST Start to find Helitron candidates.

2024年 04月 30日星期二 00:50:36 CST Identify Helitron candidates from scratch.

2024年 04月 30日星期二 00:51:01 CST Finish finding Helitron candidates.

2024年 04月 30日星期二 00:51:01 CST Execution of EDTA_raw.pl is finished!

ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.TIR.intact.raw.fa ################## It sitll got problem after reinstall,,,

Isoris commented 6 months ago

You need to provide the environment settings and your list of installed packages otherwise its hard to help

Xxi-GitHub commented 6 months ago

$ conda activate edta $ conda list

packages in environment at /home/xionglab250/mambaforge/envs/edta:

#

Name Version Build Channel

Xxi-GitHub commented 6 months ago

Thanks for your help！We have uploaded the conda env package list to github issue， did it lack any package？Or we can try another way to install？Thanks！

------------------ 原始邮件 ------------------ 发件人: "oushujun/EDTA" @.>; 发送时间: 2024年5月1日(星期三) 上午10:51 @.>; @.**@.>; 主题: Re: [oushujun/EDTA] '调用失败' (Issue #458)

You need to provide the environment settings and your list of installed packages otherwise its hard to help

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

leezhen1991 commented 6 months ago

Have you resolved your issue? I encountered a similar problem when running EDTA.

Isoris commented 6 months ago

I didn't look in detail and I am not the author of the software however for the Line and repeat modeler I found that the consensus file is created with Line sequences inside of the fasta but it seems that the consensus.fa file in LINE/ is probably not named with $genome prefix so it seems that EDTA can't read it because of its name / path

Xxi-GitHub commented 6 months ago

File "/home/xionglab250/mambaforge/envs/edta/lib/python3.9/site-packages/numpy/init.py", line 324, in getattr raise AttributeError(former_attrs[attr]) AttributeError: module 'numpy' has no attribute 'object'. np.object was a deprecated alias for the builtin object. To avoid this error in existing code, use object by itself. Doing this will not modify any behavior and is safe. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

That is part of error reports , it seems that numpy function 'object' did not work...emmmm

oushujun commented 1 month ago

The initial error Invalid value for shared scalar was solved in the LTR_retriever repo. Reinstalling EDTA should solve the issue. please refer to #497

Thanks! Shujun

leezhen1991 commented 1 month ago

Thank you very much! I will reinstall EDTA later. Lizhen

李珍 @.***

------------------ 原始邮件 ------------------ 发件人: "oushujun/EDTA" @.>; 发送时间: 2024年10月7日(星期一) 晚上9:13 @.>; @.**@.>; 主题: Re: [oushujun/EDTA] '调用失败' (Issue #458)

The initial error Invalid value for shared scalar was solved in the LTR_retriever repo. Reinstalling EDTA should solve the issue. please refer to #497

Thanks! Shujun

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

Isoris commented 1 month ago

Just use the conda version

Follow the instructions. However I noticed that sometimes the SINEs don't appear so you need to add the SINEs as -lib as in the tutorial too. Overall this EDTA version works quite well.

But I think it is a bit sad that we cannot choose what run to restart if we want to redo only one type of TE like helitron, if we do EDTA it doesn't ask us which type unless we use EDTA.raw but it's annoying to have to merge the Types of TE. It's better to let the user choose to continue an EDTA run and to redo from row only 1 superfamily

oushujun / EDTA

'调用失败' #458

packages in environment at /home/xionglab250/mambaforge/envs/edta:

Name Version Build Channel