Error in Step 4) running reasonaTE pipeline on the genome annotations

[macobam]

Hi Kevin,

I have an error in the step 4 with reasonaTE pipeline.

Damag/TE_Damag/finalResults/ToolAnnotations_Transposons.gff3    Traceback (most recent call last):
  File "/home/mcoba/miniconda3/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/TransposonAnnotator.py", line 166, in <module>
    createToolAnnotation_Files(os.path.join(arg1,arg2), os.path.join(arg1,arg2,"finalResults"), os.path.join(arg1,arg2,"parsedAnnotations"), os.path.join(arg1,arg2,"transposonCandB"), os.path.join(arg1,arg2,"transposonCandF"))
  File "/home/mcoba/miniconda3/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/FinalResultsCreator.py", line 78, in createToolAnnotation_Files
    f = open(os.path.join(folderTranspCandF,"ToolAnnotations_TransposonSequencesClasses.txt"),"r")
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'Damag/TE_Damag/transposonCandF/ToolAnnotations_TransposonSequencesClasses.txt'

I search similar topics in Issues and found this https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/issues/16, so I changed the TransposonClustering.py file in the line 184 on the folder: ~/miniconda3/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/

Although, the problem still remains, and I do not know how to get it to run this step. I kindly request your help.

Next, attach screenshots of previous steps that ran.

The annotations were done with all tools, even for RepeatModeler I had to execute your script corrector.py for the .sk output file, because also I had an error in the parse annotations step.

However, I'm surprised that step 3 didn't consider the repeatmodeler annotations because it shows 0.

Kind regards, Manuel Alejandro

[DerKevinRiehl]

Dear Manuel Alejandro, thanks for your interest in our work.

Comment on first problem: As your first error mentions, that a certain file is missing:

FileNotFoundError: [Errno 2] No such file or directory: 'Damag/TE_Damag/transposonCandF/ToolAnnotations_TransposonSequencesClasses.txt'

I am wondering if you could show me the contents of the folder transposonCandF?

Comment on second problem:

However, I'm surprised that step 3 didn't consider the repeatmodeler annotations because it shows 0.

The reason for this could be that your version of repeatmodeler maybe named files in a different way than expected by reasonaTE. Could you share with me which files exist in the folder 'Damag/TE_Damag/repeatmodel' ? As you can see in the code, reasonaTE expects a file ending with "families.stk" file. https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/main/Code/AnnotationParser.py#L1213 Do you have such a file? Consider rerunning the parsing before running step 4 again.

Best, Kevin

[macobam]

Hi Kevin,

Thanks for you for your brief answer.

About the first problem

This is the content in transposonCandF folder

About the second problem

These were my three commands that run for RepeatModeler, and RepeatMasker respectively.

BuildDatabase -name sequence_index sequence.fasta
RepeatModeler -database sequence_index -threads 32 -LTRStruct
RepeatMasker -pa 24 -lib consensi.fa. -e rmblast -dir MaskerOutput sequence.fasta

And these are some screenshots about the content inside the folders of repeatmodeler and repeatmasker

All output files were copied into repeatmodel folder inside the project folder

These were the dependencies for repeatmodeler, the program was installed in another conda env.

And a partial view of my sequence_index-families.stk file is here:

Even this sequence-index-families.stk file was used to run the corrector.py script to remove blank lines because when I was in parsing step, i had an error.

sequence_index-families.zip

For repeatmasker, these were my output files;

As above the files went to the repMasker folder inside the project, (the .gz file was also unzipped).

Kind regards, Manuel Alejandro

[DerKevinRiehl]

Hello Manuel,

about the first problem: this is how it should look like. https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/tree/main/workspace/testProject/transposonCandF So no temp files. How about you empty the content and rerun after you solved the second problem?

about your second problem: so I think the STK file looks good to me. But once again: is it really in the folder "Damag/TE_Damag/repeatmodel/sequence_index-families.stk"? ReasonaTE can only find it when it is in the folder.

Best, Kevin

[macobam]

Hi Kevin,

I hope you're doing well. I'm encountering some issues in Step 3 with the output of RepeatModeler. I deleted everything and re-run the tool, generating the "sequence_index-families.stk" file. This is all the content in my folder.

However, when I execute reasonaTE -mode parseAnnotations -projectFolder workspace -projectName Damag I get the following error:

Parse repeatModeler...
Traceback (most recent call last):
  File "/home/mcoba/miniconda3/envs/transposon_annotation_tools_env/share/TransposonAnnotator_reasonaTE/TransposonAnnotator.py", line 114, in <module>
    parseAvailableResults(projectFolderPath)
  File "/home/mcoba/miniconda3/envs/transposon_annotation_tools_env/share/TransposonAnnotator_reasonaTE/AnnotationParser.py", line 1346, in parseAvailableResults
    parseRepeatModeler(pathResDir, fastaFile, targetGFFFile, targetGFFrepe, targetFastaFile)
  File "/home/mcoba/miniconda3/envs/transposon_annotation_tools_env/share/TransposonAnnotator_reasonaTE/AnnotationParser.py", line 1255, in parseRepeatModeler
    seqTypeLabelA = seqType.split(";")[1]
IndexError: list index out of range

I ran the corrector.py script provided in #3 and #12, but neither worked. I'm not sure how to resolve this issue or if there are any recommendations for including these annotations in the pipeline. Thank you for your assistance.

Kind regards, Manuel Alejandro Coba

[DerKevinRiehl]

Hello Manuel Alejandro Coba, can you provide me with the file sequence_index-families.stk, like a small snippet of the first 100 lines?

Thanks, Kevin

[macobam]

sequence_index-families.zip

Hi Kevin, here is the first 100 lines of the sequence_index-families.stk output after running RepeatModeler. The file is compressed in a zip file. Thanks for the support.

Kind regards, Manuel Alejandro

[DerKevinRiehl]

Hello Manuel Alejandro, I think I know the problem (but I dont know for sure). Can you try following please:

1. Download this Zip file Code.zip
2. Copy the included file "AnnotationParser.py"
3. Paste it (overwrite) to the following folder on your machine: "/home/mcoba/miniconda3/envs/transposon_annotation_tools_env/share/TransposonAnnotator_reasonaTE/AnnotationParser.py"

Then run and tell me if it worked without issues. Sorry for the inconvenience and hope this helps. Looking forward to hearing back from you, Best, Kevin

[macobam]

Hello Kevin,

It worked. The parse annotation step recognizes the Repeat Modeler results although the final results did not change significantly.

I also take this opportunity to ask one more question. I understand that I could calculate the percentage of each transposon class based on the total base pairs identified by classes in the Statistics_FinalAnnotations.txt file, is that correct? My doubt is if I want to know the total percentage of transposons in my genome, is it correct to divide the base pairs of all transposons (for example, 1000 bp) by the genome length (for example, 5000 bp)? This would give me 20%. Is it the same as summing the percentages obtained in 1|Class I and 2|Class II, and so on according to the hierarchical classification?

Additionally, what would happen if I am interested in a specific family of DNA transposons, but it is only included at the maximum classification level as TIR? Could it suggest that the pipeline throughout all tools did not identify this class of transposon?

Best regards, Manuel Alejandro

[DerKevinRiehl]

Dear Manuel Alejandro, great to hear it worked, I am happy to see you proceed.

My doubt is if I want to know the total percentage of transposons in my genome, is it correct to divide the base pairs of all transposons (for example, 1000 bp) by the genome length (for example, 5000 bp)? This would give me 20%. Is it the same as summing the percentages obtained in 1|Class I and 2|Class II, and so on according to the hierarchical classification?

So I would argue that the way you describe it "percentage of transposons in genome = length in base pairs of transposons / length of genome" is a valid measure. Please be aware, that the annotations found can intersect, we therefore provide the "mask" annotation. https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/main/workspace/testProject/finalResults/FinalAnnotations_TransposonMask.gff3 So the length in base pairs of transposons = number of base pairs masked as transposon in the mask file!

Please find some statistics in the output file "https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/main/workspace/testProject/Statistics_FinalAnnotations.txt" Here we already present you the counts in basepairs of the masks (so basepairs class 1 + class 2 = all, class 1.1+1.2 = class 1, and so on...)

Additionally, what would happen if I am interested in a specific family of DNA transposons, but it is only included at the maximum classification level as TIR? Could it suggest that the pipeline throughout all tools did not identify this class of transposon?

When we were designing the software and training a model on a very large transposon database that consists of many small ones, we had to make tradeoffs as every database had a different taxonomies. This is, why at some point, the depth of transposons the classifier can distinguish is not as deep as might be desired. Therefore, the results only indicate a certain hyper-classification, without making any guesses about sub-classes.

Hope that helped. Please do not hesitate to ask further questions. Looking forward to a potential publication from you :-) Best regards, Kevin

[Riccardo1274]

Dear Kevin, sorry to bother you. I'm having the same error found in this issue: workspace_reasonaTE/te_hr/finalResults/ToolAnnotations_Transposons.gff3 Traceback (most recent call last): File "/data/rossir/bin/miniconda/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/TransposonAnnotator.py", line 166, in createToolAnnotation_Files(os.path.join(arg1,arg2), os.path.join(arg1,arg2,"finalResults"), os.path.join(arg1,arg2,"parsedAnnotations"), os.path.join(arg1,arg2,"transposonCandB"), os.path.join(arg1,arg2,"transposonCandF")) File "/data/rossir/bin/miniconda/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/FinalResultsCreator.py", line 78, in createToolAnnotation_Files f = open(os.path.join(folderTranspCandF,"ToolAnnotations_TransposonSequencesClasses.txt"),"r") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'workspace_reasonaTE/te_hr/transposonCandF/ToolAnnotations_TransposonSequencesClasses.txt'

This was the command line: nohup reasonaTE -mode pipeline -projectFolder workspace_reasonaTE/ -projectName te_hr &> te_logs/pipeline.log &

I followed all your suggestions, but, even if I clean the folder transposonCandF and rerun, I still get just these temporary files: ToolAnnotations_TransposonSequencesClasses.txt.featuresA_20240213_165009.temp ToolAnnotations_TransposonSequencesClasses.txt.featuresB_20240213_165009.temp ToolAnnotations_TransposonSequencesClasses.txt.featuresC_20240213_165009.temp I also modified TransposonsClustering.py as in #16, but nothing changed I fixed other errors by looking at the other issue (thanks for your helps!) but I can't get what I'm doing wrong with this one. Everything went good (or so it seems to me), except for this part. Your pipeline fits perfectly for my work, so I am trying to insist :) Thanks in advance. Kind regards, Riccardo Rossi

[DerKevinRiehl]

Dear Riccardo, no worries, let us investigate this issue together, I am happy to hear the pipeline is interesting and relevant to you.

What step Cand F is doing is basically to classify the transposons found.

This is what reasonaTe is doing at this step: https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/cc04a2db30c98f21981eb2d90710887be726bfcc/Code/FinalResultsCreator.py#L136 It is calling transposon annotator.

I am curious, which environment are you using? The python=3.6 environment right? If so, can you just run this command in your cmd to let us see if your transposonRFSB classifier module has /is the a problem:

• make a folder somewhere, and copy the file "finalResults/PipelineAnnotations_TransposonSequences.fasta" into it.
• then call this command (same conda environment) and tell me your console output inside the new folder

  transposon_classifier_RFSB -mode classify -fastaFile PipelineAnnotations_TransposonSequences.fasta -outputPredictionFile  PipelineAnnotations_TransposonSequencesClasses.txt

I guess reasonaTe has problems calling transposon_classifier_RFSB. Once we understand why and what the problem is, we can solve it.

Anyway, the code already produced many results for your research yet, that can be found in "finalResults" of your project Folder. The classification of the transposons is the last step missing, you are almost done.

Looking forward to your answer, Best, Kevin

[Riccardo1274]

Dear Kevin, Sorry for the late reply. After your kind help, I realised that in the enviroment python was not 3.6, and that my transposonRFSB classifier module was not installed correctly, since the command you sent me didn't work. Before proceeding with your suggestions, I changed the Python version and reinstalled the transposonRFSB classifier module. After that, your command worked, so I started step 4 of the pipeline again to see if it would work. I got the following error: seq99 Iteration 1 105 0 / 105 ... seq99 Iteration 2 32 0 / 32 ... workspace_reasonaTE/te_hr/finalResults/ToolAnnotations_Transposons.gff3 Traceback (most recent call last): File "/data/rossir/bin/miniconda/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/TransposonAnnotator.py", line 166, in createToolAnnotation_Files(os.path.join(arg1,arg2), os.path.join(arg1,arg2,"finalResults"), os.path.join(arg1,arg2,"parsedAnnotations"), os.path.join(arg1,arg2,"transposonCandB"), os.path.join(arg1,arg2,"transposonCandF")) File "/data/rossir/bin/miniconda/envs/transposon_annotation_reasonaTE/share/TransposonAnnotator_reasonaTE/FinalResultsCreator.py", line 78, in createToolAnnotation_Files f = open(os.path.join(folderTranspCandF,"ToolAnnotations_TransposonSequencesClasses.txt"),"r") FileNotFoundError: [Errno 2] No such file or directory: 'workspace_reasonaTE/te_hr/transposonCandF/ToolAnnotations_TransposonSequencesClasses.txt' It is very similar to the previous one, so even with the correct installation not much has changed.

I have done as you asked. I'll show you the result

Many thanks again. Kind regards, Riccardo Rossi

[DerKevinRiehl]

Dear Riccardo, can you run the command without reasonaTE directly?

• make a folder somewhere, and copy the file "finalResults/PipelineAnnotations_TransposonSequences.fasta" into it.
• then call this command (same conda environment) and tell me your console output inside the new folder

  transposon_classifier_RFSB -mode classify -fastaFile PipelineAnnotations_TransposonSequences.fasta -outputPredictionFile  PipelineAnnotations_TransposonSequencesClasses.txt

  Let me know if you successfully produce a file.

Best, Kevin

[Riccardo1274]

Dear Kevin, I am sorry, I don't know if I got your message right.

Here's what I did

Here's the resulting file

PipelineAnnotations_TransposonSequencesClasses.txt

Did you want to install transposon_classifier_RFSB out of reasonaTE and try the command?

Thank you again for your patience. Best regards, Riccardo Rossi

[DerKevinRiehl]

Dear Riccardo, great to hear that transposon_classifier_RFSB worked on your machine separately from reasonaTE :-).

Next Step 1: Now you have the file "PipelineAnnotations_TransposonSequencesClasses.txt" , rename it and paste in the folder _transposonCandF/ToolAnnotationsTransposonSequencesClasses.txt of your reasonaTE project.

Next Step 2: Please run resonaTE again, and let us see if it runs through now.

Best regards, Kevin

[Riccardo1274]

Dear Kevin, my finalResults folder doesn't contain PipelineAnnotations_TransposonSequences.fasta. The file I used above was taken from your directory (workspace/testProject/finalResults). Here's what I have: That may be the problem actually. Am I doing something wrong? Many thanks again. Kind regards, Riccardo Rossi

[DerKevinRiehl]

Dear Riccardo, thanks for this info! So now we need to investigate why you dont have _PipelineAnnotationsTransposonSequences.fasta in the first place.

Can you please show me the content of these folders?

• transposonCandA
• transposonCandB
• transposonCandE
• transposonCandF

Thanks, Kevin

[Riccardo1274]

Dear Kevin, thanks again. Here's the folders content. This is transposonCandB: ls ../transposonCandB CandidatesB_0.gff3 CandidatesB_it225.gff3 CandidatesB_it352.gff3 CandidatesB_it47.gff3 CandidatesB_1.gff3 CandidatesB_it226.gff3 CandidatesB_it353.gff3 CandidatesB_it480.gff3 CandidatesB_it0.gff3 CandidatesB_it227.gff3 CandidatesB_it354.gff3 CandidatesB_it481.gff3 CandidatesB_it100.gff3 CandidatesB_it228.gff3 CandidatesB_it355.gff3 CandidatesB_it482.gff3 CandidatesB_it101.gff3 CandidatesB_it229.gff3 CandidatesB_it356.gff3 CandidatesB_it483.gff3 CandidatesB_it102.gff3 CandidatesB_it22.gff3 CandidatesB_it357.gff3 CandidatesB_it484.gff3 CandidatesB_it103.gff3 CandidatesB_it230.gff3 CandidatesB_it358.gff3 CandidatesB_it485.gff3 CandidatesB_it104.gff3 CandidatesB_it231.gff3 CandidatesB_it359.gff3 CandidatesB_it486.gff3 CandidatesB_it105.gff3 CandidatesB_it232.gff3 CandidatesB_it35.gff3 CandidatesB_it487.gff3 CandidatesB_it106.gff3 CandidatesB_it233.gff3 CandidatesB_it360.gff3 CandidatesB_it488.gff3 CandidatesB_it107.gff3 CandidatesB_it234.gff3 CandidatesB_it361.gff3 CandidatesB_it489.gff3 CandidatesB_it108.gff3 CandidatesB_it235.gff3 CandidatesB_it362.gff3 CandidatesB_it48.gff3 CandidatesB_it109.gff3 CandidatesB_it236.gff3 CandidatesB_it363.gff3 CandidatesB_it490.gff3 CandidatesB_it10.gff3 CandidatesB_it237.gff3 CandidatesB_it364.gff3 CandidatesB_it491.gff3 CandidatesB_it110.gff3 CandidatesB_it238.gff3 CandidatesB_it365.gff3 CandidatesB_it492.gff3 CandidatesB_it111.gff3 CandidatesB_it239.gff3 CandidatesB_it366.gff3 CandidatesB_it493.gff3 CandidatesB_it112.gff3 CandidatesB_it23.gff3 CandidatesB_it367.gff3 CandidatesB_it494.gff3 CandidatesB_it113.gff3 CandidatesB_it240.gff3 CandidatesB_it368.gff3 CandidatesB_it495.gff3 CandidatesB_it114.gff3 CandidatesB_it241.gff3 CandidatesB_it369.gff3 CandidatesB_it496.gff3 CandidatesB_it115.gff3 CandidatesB_it242.gff3 CandidatesB_it36.gff3 CandidatesB_it497.gff3 CandidatesB_it116.gff3 CandidatesB_it243.gff3 CandidatesB_it370.gff3 CandidatesB_it498.gff3 CandidatesB_it117.gff3 CandidatesB_it244.gff3 CandidatesB_it371.gff3 CandidatesB_it499.gff3 CandidatesB_it118.gff3 CandidatesB_it245.gff3 CandidatesB_it372.gff3 CandidatesB_it49.gff3 CandidatesB_it119.gff3 CandidatesB_it246.gff3 CandidatesB_it373.gff3 CandidatesB_it4.gff3 CandidatesB_it11.gff3 CandidatesB_it247.gff3 CandidatesB_it374.gff3 CandidatesB_it500.gff3 CandidatesB_it120.gff3 CandidatesB_it248.gff3 CandidatesB_it375.gff3 CandidatesB_it501.gff3 CandidatesB_it121.gff3 CandidatesB_it249.gff3 CandidatesB_it376.gff3 CandidatesB_it502.gff3 CandidatesB_it122.gff3 CandidatesB_it24.gff3 CandidatesB_it377.gff3 CandidatesB_it503.gff3 CandidatesB_it123.gff3 CandidatesB_it250.gff3 CandidatesB_it378.gff3 CandidatesB_it504.gff3 CandidatesB_it124.gff3 CandidatesB_it251.gff3 CandidatesB_it379.gff3 CandidatesB_it505.gff3 CandidatesB_it125.gff3 CandidatesB_it252.gff3 CandidatesB_it37.gff3 CandidatesB_it506.gff3 CandidatesB_it126.gff3 CandidatesB_it253.gff3 CandidatesB_it380.gff3 CandidatesB_it507.gff3 CandidatesB_it127.gff3 CandidatesB_it254.gff3 CandidatesB_it381.gff3 CandidatesB_it508.gff3 CandidatesB_it128.gff3 CandidatesB_it255.gff3 CandidatesB_it382.gff3 CandidatesB_it509.gff3 CandidatesB_it129.gff3 CandidatesB_it256.gff3 CandidatesB_it383.gff3 CandidatesB_it50.gff3 CandidatesB_it12.gff3 CandidatesB_it257.gff3 CandidatesB_it384.gff3 CandidatesB_it510.gff3 CandidatesB_it130.gff3 CandidatesB_it258.gff3 CandidatesB_it385.gff3 CandidatesB_it511.gff3 CandidatesB_it131.gff3 CandidatesB_it259.gff3 CandidatesB_it386.gff3 CandidatesB_it512.gff3 CandidatesB_it132.gff3 CandidatesB_it25.gff3 CandidatesB_it387.gff3 CandidatesB_it513.gff3 CandidatesB_it133.gff3 CandidatesB_it260.gff3 CandidatesB_it388.gff3 CandidatesB_it514.gff3 CandidatesB_it134.gff3 CandidatesB_it261.gff3 CandidatesB_it389.gff3 CandidatesB_it515.gff3 CandidatesB_it135.gff3 CandidatesB_it262.gff3 CandidatesB_it38.gff3 CandidatesB_it516.gff3 CandidatesB_it136.gff3 CandidatesB_it263.gff3 CandidatesB_it390.gff3 CandidatesB_it517.gff3 CandidatesB_it137.gff3 CandidatesB_it264.gff3 CandidatesB_it391.gff3 CandidatesB_it518.gff3 CandidatesB_it138.gff3 CandidatesB_it265.gff3 CandidatesB_it392.gff3 CandidatesB_it519.gff3 CandidatesB_it139.gff3 CandidatesB_it266.gff3 CandidatesB_it393.gff3 CandidatesB_it51.gff3 CandidatesB_it13.gff3 CandidatesB_it267.gff3 CandidatesB_it394.gff3 CandidatesB_it520.gff3 CandidatesB_it140.gff3 CandidatesB_it268.gff3 CandidatesB_it395.gff3 CandidatesB_it521.gff3 CandidatesB_it141.gff3 CandidatesB_it269.gff3 CandidatesB_it396.gff3 CandidatesB_it522.gff3 CandidatesB_it142.gff3 CandidatesB_it26.gff3 CandidatesB_it397.gff3 CandidatesB_it523.gff3 CandidatesB_it143.gff3 CandidatesB_it270.gff3 CandidatesB_it398.gff3 CandidatesB_it524.gff3 CandidatesB_it144.gff3 CandidatesB_it271.gff3 CandidatesB_it399.gff3 CandidatesB_it525.gff3 CandidatesB_it145.gff3 CandidatesB_it272.gff3 CandidatesB_it39.gff3 CandidatesB_it526.gff3 CandidatesB_it146.gff3 CandidatesB_it273.gff3 CandidatesB_it3.gff3 CandidatesB_it527.gff3 CandidatesB_it147.gff3 CandidatesB_it274.gff3 CandidatesB_it400.gff3 CandidatesB_it528.gff3 CandidatesB_it148.gff3 CandidatesB_it275.gff3 CandidatesB_it401.gff3 CandidatesB_it529.gff3 CandidatesB_it149.gff3 CandidatesB_it276.gff3 CandidatesB_it402.gff3 CandidatesB_it52.gff3 CandidatesB_it14.gff3 CandidatesB_it277.gff3 CandidatesB_it403.gff3 CandidatesB_it530.gff3 CandidatesB_it150.gff3 CandidatesB_it278.gff3 CandidatesB_it404.gff3 CandidatesB_it531.gff3 CandidatesB_it151.gff3 CandidatesB_it279.gff3 CandidatesB_it405.gff3 CandidatesB_it532.gff3 CandidatesB_it152.gff3 CandidatesB_it27.gff3 CandidatesB_it406.gff3 CandidatesB_it533.gff3 CandidatesB_it153.gff3 CandidatesB_it280.gff3 CandidatesB_it407.gff3 CandidatesB_it534.gff3 CandidatesB_it154.gff3 CandidatesB_it281.gff3 CandidatesB_it408.gff3 CandidatesB_it535.gff3 CandidatesB_it155.gff3 CandidatesB_it282.gff3 CandidatesB_it409.gff3 CandidatesB_it536.gff3 CandidatesB_it156.gff3 CandidatesB_it283.gff3 CandidatesB_it40.gff3 CandidatesB_it537.gff3 CandidatesB_it157.gff3 CandidatesB_it284.gff3 CandidatesB_it410.gff3 CandidatesB_it538.gff3 CandidatesB_it158.gff3 CandidatesB_it285.gff3 CandidatesB_it411.gff3 CandidatesB_it539.gff3 CandidatesB_it159.gff3 CandidatesB_it286.gff3 CandidatesB_it412.gff3 CandidatesB_it53.gff3 CandidatesB_it15.gff3 CandidatesB_it287.gff3 CandidatesB_it413.gff3 CandidatesB_it540.gff3 CandidatesB_it160.gff3 CandidatesB_it288.gff3 CandidatesB_it414.gff3 CandidatesB_it541.gff3 CandidatesB_it161.gff3 CandidatesB_it289.gff3 CandidatesB_it415.gff3 CandidatesB_it542.gff3 CandidatesB_it162.gff3 CandidatesB_it28.gff3 CandidatesB_it416.gff3 CandidatesB_it543.gff3 CandidatesB_it163.gff3 CandidatesB_it290.gff3 CandidatesB_it417.gff3 CandidatesB_it544.gff3 CandidatesB_it164.gff3 CandidatesB_it291.gff3 CandidatesB_it418.gff3 CandidatesB_it545.gff3 CandidatesB_it165.gff3 CandidatesB_it292.gff3 CandidatesB_it419.gff3 CandidatesB_it546.gff3 CandidatesB_it166.gff3 CandidatesB_it293.gff3 CandidatesB_it41.gff3 CandidatesB_it547.gff3 CandidatesB_it167.gff3 CandidatesB_it294.gff3 CandidatesB_it420.gff3 CandidatesB_it548.gff3 CandidatesB_it168.gff3 CandidatesB_it295.gff3 CandidatesB_it421.gff3 CandidatesB_it549.gff3 CandidatesB_it169.gff3 CandidatesB_it296.gff3 CandidatesB_it422.gff3 CandidatesB_it54.gff3 CandidatesB_it16.gff3 CandidatesB_it297.gff3 CandidatesB_it423.gff3 CandidatesB_it550.gff3 CandidatesB_it170.gff3 CandidatesB_it298.gff3 CandidatesB_it424.gff3 CandidatesB_it551.gff3 CandidatesB_it171.gff3 CandidatesB_it299.gff3 CandidatesB_it425.gff3 CandidatesB_it552.gff3 CandidatesB_it172.gff3 CandidatesB_it29.gff3 CandidatesB_it426.gff3 CandidatesB_it553.gff3 CandidatesB_it173.gff3 CandidatesB_it2.gff3 CandidatesB_it427.gff3 CandidatesB_it554.gff3 CandidatesB_it174.gff3 CandidatesB_it300.gff3 CandidatesB_it428.gff3 CandidatesB_it555.gff3 CandidatesB_it175.gff3 CandidatesB_it301.gff3 CandidatesB_it429.gff3 CandidatesB_it556.gff3 CandidatesB_it176.gff3 CandidatesB_it302.gff3 CandidatesB_it42.gff3 CandidatesB_it557.gff3 CandidatesB_it177.gff3 CandidatesB_it303.gff3 CandidatesB_it430.gff3 CandidatesB_it558.gff3 CandidatesB_it178.gff3 CandidatesB_it304.gff3 CandidatesB_it431.gff3 CandidatesB_it559.gff3 CandidatesB_it179.gff3 CandidatesB_it305.gff3 CandidatesB_it432.gff3 CandidatesB_it55.gff3 CandidatesB_it17.gff3 CandidatesB_it306.gff3 CandidatesB_it433.gff3 CandidatesB_it560.gff3 CandidatesB_it180.gff3 CandidatesB_it307.gff3 CandidatesB_it434.gff3 CandidatesB_it561.gff3 CandidatesB_it181.gff3 CandidatesB_it308.gff3 CandidatesB_it435.gff3 CandidatesB_it56.gff3 CandidatesB_it182.gff3 CandidatesB_it309.gff3 CandidatesB_it436.gff3 CandidatesB_it57.gff3 CandidatesB_it183.gff3 CandidatesB_it30.gff3 CandidatesB_it437.gff3 CandidatesB_it58.gff3 CandidatesB_it184.gff3 CandidatesB_it310.gff3 CandidatesB_it438.gff3 CandidatesB_it59.gff3 CandidatesB_it185.gff3 CandidatesB_it311.gff3 CandidatesB_it439.gff3 CandidatesB_it5.gff3 CandidatesB_it186.gff3 CandidatesB_it312.gff3 CandidatesB_it43.gff3 CandidatesB_it60.gff3 CandidatesB_it187.gff3 CandidatesB_it313.gff3 CandidatesB_it440.gff3 CandidatesB_it61.gff3 CandidatesB_it188.gff3 CandidatesB_it314.gff3 CandidatesB_it441.gff3 CandidatesB_it62.gff3 CandidatesB_it189.gff3 CandidatesB_it315.gff3 CandidatesB_it442.gff3 CandidatesB_it63.gff3 CandidatesB_it18.gff3 CandidatesB_it316.gff3 CandidatesB_it443.gff3 CandidatesB_it64.gff3 CandidatesB_it190.gff3 CandidatesB_it317.gff3 CandidatesB_it444.gff3 CandidatesB_it65.gff3 CandidatesB_it191.gff3 CandidatesB_it318.gff3 CandidatesB_it445.gff3 CandidatesB_it66.gff3 CandidatesB_it192.gff3 CandidatesB_it319.gff3 CandidatesB_it446.gff3 CandidatesB_it67.gff3 CandidatesB_it193.gff3 CandidatesB_it31.gff3 CandidatesB_it447.gff3 CandidatesB_it68.gff3 CandidatesB_it194.gff3 CandidatesB_it320.gff3 CandidatesB_it448.gff3 CandidatesB_it69.gff3 CandidatesB_it195.gff3 CandidatesB_it321.gff3 CandidatesB_it449.gff3 CandidatesB_it6.gff3 CandidatesB_it196.gff3 CandidatesB_it322.gff3 CandidatesB_it44.gff3 CandidatesB_it70.gff3 CandidatesB_it197.gff3 CandidatesB_it323.gff3 CandidatesB_it450.gff3 CandidatesB_it71.gff3 CandidatesB_it198.gff3 CandidatesB_it324.gff3 CandidatesB_it451.gff3 CandidatesB_it72.gff3 CandidatesB_it199.gff3 CandidatesB_it325.gff3 CandidatesB_it452.gff3 CandidatesB_it73.gff3 CandidatesB_it19.gff3 CandidatesB_it326.gff3 CandidatesB_it453.gff3 CandidatesB_it74.gff3 CandidatesB_it1.gff3 CandidatesB_it327.gff3 CandidatesB_it454.gff3 CandidatesB_it75.gff3 CandidatesB_it200.gff3 CandidatesB_it328.gff3 CandidatesB_it455.gff3 CandidatesB_it76.gff3 CandidatesB_it201.gff3 CandidatesB_it329.gff3 CandidatesB_it456.gff3 CandidatesB_it77.gff3 CandidatesB_it202.gff3 CandidatesB_it32.gff3 CandidatesB_it457.gff3 CandidatesB_it78.gff3 CandidatesB_it203.gff3 CandidatesB_it330.gff3 CandidatesB_it458.gff3 CandidatesB_it79.gff3 CandidatesB_it204.gff3 CandidatesB_it331.gff3 CandidatesB_it459.gff3 CandidatesB_it7.gff3 CandidatesB_it205.gff3 CandidatesB_it332.gff3 CandidatesB_it45.gff3 CandidatesB_it80.gff3 CandidatesB_it206.gff3 CandidatesB_it333.gff3 CandidatesB_it460.gff3 CandidatesB_it81.gff3 CandidatesB_it207.gff3 CandidatesB_it334.gff3 CandidatesB_it461.gff3 CandidatesB_it82.gff3 CandidatesB_it208.gff3 CandidatesB_it335.gff3 CandidatesB_it462.gff3 CandidatesB_it83.gff3 CandidatesB_it209.gff3 CandidatesB_it336.gff3 CandidatesB_it463.gff3 CandidatesB_it84.gff3 CandidatesB_it20.gff3 CandidatesB_it337.gff3 CandidatesB_it464.gff3 CandidatesB_it85.gff3 CandidatesB_it210.gff3 CandidatesB_it338.gff3 CandidatesB_it465.gff3 CandidatesB_it86.gff3 CandidatesB_it211.gff3 CandidatesB_it339.gff3 CandidatesB_it466.gff3 CandidatesB_it87.gff3 CandidatesB_it212.gff3 CandidatesB_it33.gff3 CandidatesB_it467.gff3 CandidatesB_it88.gff3 CandidatesB_it213.gff3 CandidatesB_it340.gff3 CandidatesB_it468.gff3 CandidatesB_it89.gff3 CandidatesB_it214.gff3 CandidatesB_it341.gff3 CandidatesB_it469.gff3 CandidatesB_it8.gff3 CandidatesB_it215.gff3 CandidatesB_it342.gff3 CandidatesB_it46.gff3 CandidatesB_it90.gff3 CandidatesB_it216.gff3 CandidatesB_it343.gff3 CandidatesB_it470.gff3 CandidatesB_it91.gff3 CandidatesB_it217.gff3 CandidatesB_it344.gff3 CandidatesB_it471.gff3 CandidatesB_it92.gff3 CandidatesB_it218.gff3 CandidatesB_it345.gff3 CandidatesB_it472.gff3 CandidatesB_it93.gff3 CandidatesB_it219.gff3 CandidatesB_it346.gff3 CandidatesB_it473.gff3 CandidatesB_it94.gff3 CandidatesB_it21.gff3 CandidatesB_it347.gff3 CandidatesB_it474.gff3 CandidatesB_it95.gff3 CandidatesB_it220.gff3 CandidatesB_it348.gff3 CandidatesB_it475.gff3 CandidatesB_it96.gff3 CandidatesB_it221.gff3 CandidatesB_it349.gff3 CandidatesB_it476.gff3 CandidatesB_it97.gff3 CandidatesB_it222.gff3 CandidatesB_it34.gff3 CandidatesB_it477.gff3 CandidatesB_it98.gff3 CandidatesB_it223.gff3 CandidatesB_it350.gff3 CandidatesB_it478.gff3 CandidatesB_it99.gff3 CandidatesB_it224.gff3 CandidatesB_it351.gff3 CandidatesB_it479.gff3 CandidatesB_it9.gff3

Kind regards, Riccardo Rossi

[Riccardo1274]

Dear Kevin, On my last attempt, I reinstalled everything in a new conda environment. I don't know what went wrong, but it worked perfectly now. Thank you for your kindness and help, Riccardo Rossi

[DerKevinRiehl]

Dear Riccardo, great to hear it worked now :-)

Unfortunately conda is not what it used to be, but sometimes reinstallation can really do the trick. Please reopen or create new issue if you have any problem. Best, Kevin