Issue with mamba

[Ramkyeri]

Dear Kevin Riehl,

I have the issue, both conda and mamba have issue with my system.

As you mentioned I used 2.7, but it shows conflict

[Ramkyeri]

Dear Kevin Riehl,

I am getting the same issue even after moving to ubuntu 20.

[DerKevinRiehl]

Dear Ramkyeri,
in the titel of this post you mention "issue with mamba" but in your screenshots you use conda to install, not mamba.
As the conda package management system evolved over time it got really slow.
How about you try mamba?

Best, Kevin

[Ramkyeri]

Dear Kevin,

Many thanks for your reply. I tried both conda and mamba, but both had issue with following error

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

feature:/linux-64::__glibc==2.31=0
python=2.7 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.31"

However, I have installed the package using this command

"conda create -y -c conda-forge -c bioconda -c derkevinriehl -p transposon_annotation_tools_env/ python=2.7 mamba conda genometools-genometools transposon_annotation_toolsd1000 transposon_annotation_tools_transposonpsicli transposon_annotation_tools_mitetracker transposon_annotation_tools_helitronscanner transposon_annotation_tools_mitefinderii transposon_annotation_tools_mustv2 transposon_annotation_tools_sinefinder transposon_annotation_tools_sinescan=1.1.2 transposon_annotation_reasonate"

I hope that command will run without error, or I am planning to use docker.

Still I need to install "RepeatMasker" and "RepeatModeler, but it is not eassy.

with regards

[DerKevinRiehl]

Ah okay, great to hear you made some progress :-)

Yes, I agree, it is really not easy to deal with all the different software packages on linux and different environments.

Looking forward to hear from any further steps towards to success,
Best, Kevin

[Ramkyeri]

Dear Kevin,

I checked yml file, you did not include RepeatMasker" and "RepeatModeler. I thought that it will available in docker.

[Ramkyeri]

Dear Kevin,

could I use this one "https://github.com/Dfam-consortium/TETools" to run RepeatMasker" and "RepeatModeler.

Dfam-consortium/TETools#28 (comment)

[Ramkyeri]

Dear Kevin,

what is the running time for the demo file, reasonaTE runs with your demo file for more than 48 hours.

[DerKevinRiehl]

Dear Ramkyeri,
it really depends on what machine / computer cluster you use.
Also it depends which step you run.

Could you please be more specific and tell us which step takes so long / you are at?

Best regards, Kevin

[Ramkyeri]

Dear Kevin,

I am also getting this kind of error

I am also running now RepeatModeler,

[Ramkyeri]

Dear Kevin,

this is the final results, now I wonder which one is final GFF file, becasue there are many files are there in results folder.

column 6 represnets what?

[DerKevinRiehl]

Dear Ramkyeri,

you can find the outputfiles and their meanings in the documentation of reasonaTE
https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE#documentation-of-output-files

As you can see in the standard of GFF https://en.wikipedia.org/wiki/General_feature_format you find which column means what.
"6 | score | Numeric value that generally indicates the confidence of the source in the annotated feature. A value of "." (a dot) is used to define a null value."

[Ramkyeri]

Dear Ramkyeri,

you can find the outputfiles and their meanings in the documentation of reasonaTE https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE#documentation-of-output-files

As you can see in the standard of GFF https://en.wikipedia.org/wiki/General_feature_format you find which column means what. "6 | score | Numeric value that generally indicates the confidence of the source in the annotated feature. A value of "." (a dot) is used to define a null value."

Dear Kevin thank you so much for your kind reply.

with regards

[Ramkyeri]

Dear Kevin,

I am also confused with PipelineAnnotations and ToolAnnotations.

Introduction The outputs of the pipeline consist of mainly two parts:

Tool Annotations = merging the annotations by annotation software tools
Pipeline Annotations = Tool annotations + additional copies found in the genome.

Your software is a kind pipeline. Could you give me some suggestion.

with regards

[Ramkyeri]

Dear Kevin,
I also run the LTRpred in docoker and got the following results.
Should I copy all the filles or only any specific fiels to reasona TE
(Fworkspace\testProject\ltrPred), thanks for your kind reply.

with regards

[Ramkyeri]

Dear Kevin,
Just I copied the folder sequence_ltrdigest from ltrpred. reasona TE also considered the results.

with regards

[DerKevinRiehl]

Dear Kevin,

I am also confused with PipelineAnnotations and ToolAnnotations.

Introduction The outputs of the pipeline consist of mainly two parts:

Tool Annotations = merging the annotations by annotation software tools Pipeline Annotations = Tool annotations + additional copies found in the genome.

Your software is a kind pipeline. Could you give me some suggestion.

with regards

Hi Ramkyeri,
Tool annotations = annotations by the many tools that were developed by other researchers before (please read our paper or have a look on all the tools on this page) https://github.com/DerKevinRiehl/transposon_annotation_tools

Pipeline Annotations = our algorithm / software we developed. our software combines the findings of the many different tool annoations, and additional applies logic to find furtehr annotations.

So if you are just interested in the final results of reasonaTE, you can use the pipeline annotations.

[Ramkyeri]

Dear Kevin,
I am also confused with PipelineAnnotations and ToolAnnotations.
Introduction The outputs of the pipeline consist of mainly two parts:
Tool Annotations = merging the annotations by annotation software tools Pipeline Annotations = Tool annotations + additional copies found in the genome.
Your software is a kind pipeline. Could you give me some suggestion.
with regards

Hi Ramkyeri, Tool annotations = annotations by the many tools that were developed by other researchers before (please read our paper or have a look on all the tools on this page) https://github.com/DerKevinRiehl/transposon_annotation_tools

Pipeline Annotations = our algorithm / software we developed. our software combines the findings of the many different tool annoations, and additional applies logic to find furtehr annotations.

So if you are just interested in the final results of reasonaTE, you can use the pipeline annotations.

Dear Kevin, many thanks for your kind reply.

I need GFF file. like developed from RepeatMasker and RepeatModeler.

Thank you

with regards

[DerKevinRiehl]

Dear Kevin, I also run the LTRpred in docoker and got the following results. Should I copy all the filles or only any specific fiels to reasona TE (Fworkspace\testProject\ltrPred), thanks for your kind reply.

with regards

Hello Ramkeyri,
I recommend you look in the example project, there you can see what reasonaTE will require from LTRpred and from which folder exactly:
https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/tree/main/workspace/testProject/ltrPred

Should look like that with the same file names after copying.
From your screenshot I can see the filenames and subfolders look exactly like in the example project.

Best, Kevin

[DerKevinRiehl]

Dear Kevin, Just I copied the folder sequence_ltrdigest from ltrpred. reasona TE also considered the results.

with regards

Great :-)

[DerKevinRiehl]

Dear Kevin,
I am also confused with PipelineAnnotations and ToolAnnotations.
Introduction The outputs of the pipeline consist of mainly two parts:
Tool Annotations = merging the annotations by annotation software tools Pipeline Annotations = Tool annotations + additional copies found in the genome.
Your software is a kind pipeline. Could you give me some suggestion.
with regards

Hi Ramkyeri, Tool annotations = annotations by the many tools that were developed by other researchers before (please read our paper or have a look on all the tools on this page) https://github.com/DerKevinRiehl/transposon_annotation_tools
Pipeline Annotations = our algorithm / software we developed. our software combines the findings of the many different tool annoations, and additional applies logic to find furtehr annotations.
So if you are just interested in the final results of reasonaTE, you can use the pipeline annotations.

Dear Kevin, many thanks for your kind reply.

I need GFF file. like developed from RepeatMasker and RepeatModeler.

Thank you

with regards

Then I recommend you go in the folder "finalResults" and take "FinalAnnotations_Transposons.gff3" which is similar file type like RepeatModeler and RepeatMasker produce
https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/main/workspace/testProject/finalResults/FinalAnnotations_Transposons.gff3

Best, Kevin

[Ramkyeri]

Dear Kevin,

Thank you so much for your kind reply. I understood how to use TransposonUltimate (mainly reasona TE and deTEct).

It is a great tool. Still I have issue with RepeatModeler and RepeatMasker. I am checking both tools in docker environement.

I will update you.

with regards