error running the processConservation

[YujingLin123]

error running the processConservation Hi Idan, I have a problem when I run processConservation, I don't know how to resolve the error is :"Subroutine overlap redefined at scripts/Mapping.pm line 364.Unknown option: just-family-alignment". Could you help me? I have much thanks to you. Best, Yujing

[YujingLin123]

Hi Idan, My code is :"perl ./Conservatory/processConservation --reference species --just-family-alignment --threads 10 --conservatoryDirectory ." Best, Yujing

[YujingLin123]

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

[autumn205947]

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

hi Yujing, I'm also experiencing this problem now, can you solve this error? I look forward your reply. Thanks. Best, Autumn

[YujingLin123]

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

hi Yujing, I'm also experiencing this problem now, can you solve this error? I look forward your reply. Thanks. Best, Autumn

hi Autumn, Please accept my apologies for the delayed response. I have successfully got files in genomes directory, include: orthologs files and regulatory sequence database from processGenomes. Additionally, I have utilized the EasySpeciesTree.py script to generate a phylogenetic tree in Newick format. I would like to inquire if it is necessary for me to run phyloP to obtain .mod? However, I could not found the processConservation. Would it be possible for you to provide access to this or release it for my use? Much Thanks, Yujing

[YujingLin123]

hi Autumn,

Please accept my apologies for the delayed response. I have successfully got files in genomes directory, include: orthologs files and regulatory sequence database from processGenomes. Additionally, I have utilized the EasySpeciesTree.py script to generate a phylogenetic tree in Newick format. I would like to inquire if it is necessary for me to run phyloP to obtain .mod? However, I could not found the processConservation. Would it be possible for you to provide access to this or release it for my use?MuchThanks.

Best,

Yujing

At 2024-05-31 18:36:00, "autumn205947" @.***> wrote:

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

hi Yujing, I'm also experiencing this problem now, can you solve this error? I look forward your reply. Thanks. Best, Autumn

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

[YujingLin123]

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

hi Yujing, I'm also experiencing this problem now, can you solve this error? I look forward your reply. Thanks. Best, Autumn

hi Autumn, Please accept my apologies for the delayed response. I have successfully got files in genomes directory, include: orthologs files and regulatory sequence database from processGenomes. Additionally, I have utilized the EasySpeciesTree.py script to generate a phylogenetic tree in Newick format. I would like to inquire if it is necessary for me to run phyloP to obtain .mod? However, I could not found the processConservation. Would it be possible for you to provide access to this or release it for my use? Much Thanks, Yujing

Hi Autumn, I am currently engaged in a comparative analysis of orthologous relationships among different families using processGenomes. Is it necessary to construct a phylogenetic tree that encompasses all the species within the scope of my study? I look forward your reply. Best, Yujing

[YujingLin123]

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

hi Yujing, I'm also experiencing this problem now, can you solve this error? I look forward your reply. Thanks. Best, Autumn

hi Autumn, I attempted to run 'buildConservation' using a locus from the reference genome for the family, but the result was an empty folder. Now, upon trying 'processConservation', I encountered the same issue with an empty directory, and I am uncertain as to why this has occurred. Best, Yujing

[YujingLin123]

hi Autumn,

I attempted to run 'buildConservation' using a locus from the reference genome for the family, but the result was an empty folder. Now, upon trying 'processConservation', I encountered the same issue with an empty directory, and I am uncertain as to why this has occurred.

Best,

Yujing

At 2024-07-30 21:09:35, "YuJing Lin" @.***> wrote:

hi Autumn,

Please accept my apologies for the delayed response. I have successfully got files in genomes directory, include: orthologs files and regulatory sequence database from processGenomes. Additionally, I have utilized the EasySpeciesTree.py script to generate a phylogenetic tree in Newick format. I would like to inquire if it is necessary for me to run phyloP to obtain .mod? However, I could not found the processConservation. Would it be possible for you to provide access to this or release it for my use?MuchThanks.

Best,

Yujing

At 2024-05-31 18:36:00, "autumn205947" @.***> wrote:

Hi Idan, In addition, The .orthologs.csv is empty when I run the processGenomes (this is the code: perl ./Conservatory/processGenomes --reference species --genome-database genome_database.csv --conservatory-dir . ), I have already prepare the genome fasta file (bziped), an annotation GFF3 file and the protein sequence file for running processGenomes. Do you know why. I look forward your reply. Thanks. Best, Yujing

hi Yujing, I'm also experiencing this problem now, can you solve this error? I look forward your reply. Thanks. Best, Autumn

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