-
Notifications
You must be signed in to change notification settings - Fork 56
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
AGAT not working in perl 5.38 #416
Comments
|
@kbipinkumar Could you follow this issue? |
could you please elaborate which file provides this library? $ pacman -Ql agat
agat /usr/
agat /usr/bin/
agat /usr/bin/vendor_perl/
agat /usr/bin/vendor_perl/agat
agat /usr/bin/vendor_perl/agat_convert_bed2gff.pl
agat /usr/bin/vendor_perl/agat_convert_embl2gff.pl
agat /usr/bin/vendor_perl/agat_convert_genscan2gff.pl
agat /usr/bin/vendor_perl/agat_convert_mfannot2gff.pl
agat /usr/bin/vendor_perl/agat_convert_minimap2_bam2gff.pl
agat /usr/bin/vendor_perl/agat_convert_sp_gff2bed.pl
agat /usr/bin/vendor_perl/agat_convert_sp_gff2gtf.pl
agat /usr/bin/vendor_perl/agat_convert_sp_gff2tsv.pl
agat /usr/bin/vendor_perl/agat_convert_sp_gff2zff.pl
agat /usr/bin/vendor_perl/agat_convert_sp_gxf2gxf.pl
agat /usr/bin/vendor_perl/agat_sp_Prokka_inferNameFromAttributes.pl
agat /usr/bin/vendor_perl/agat_sp_add_attribute_shortest_exon_size.pl
agat /usr/bin/vendor_perl/agat_sp_add_attribute_shortest_intron_size.pl
agat /usr/bin/vendor_perl/agat_sp_add_intergenic_regions.pl
agat /usr/bin/vendor_perl/agat_sp_add_introns.pl
agat /usr/bin/vendor_perl/agat_sp_add_splice_sites.pl
agat /usr/bin/vendor_perl/agat_sp_add_start_and_stop.pl
agat /usr/bin/vendor_perl/agat_sp_alignment_output_style.pl
agat /usr/bin/vendor_perl/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl
agat /usr/bin/vendor_perl/agat_sp_compare_two_BUSCOs.pl
agat /usr/bin/vendor_perl/agat_sp_compare_two_annotations.pl
agat /usr/bin/vendor_perl/agat_sp_complement_annotations.pl
agat /usr/bin/vendor_perl/agat_sp_ensembl_output_style.pl
agat /usr/bin/vendor_perl/agat_sp_extract_attributes.pl
agat /usr/bin/vendor_perl/agat_sp_extract_sequences.pl
agat /usr/bin/vendor_perl/agat_sp_filter_by_ORF_size.pl
agat /usr/bin/vendor_perl/agat_sp_filter_by_locus_distance.pl
agat /usr/bin/vendor_perl/agat_sp_filter_by_mrnaBlastValue.pl
agat /usr/bin/vendor_perl/agat_sp_filter_feature_by_attribute_presence.pl
agat /usr/bin/vendor_perl/agat_sp_filter_feature_by_attribute_value.pl
agat /usr/bin/vendor_perl/agat_sp_filter_feature_from_keep_list.pl
agat /usr/bin/vendor_perl/agat_sp_filter_feature_from_kill_list.pl
agat /usr/bin/vendor_perl/agat_sp_filter_gene_by_intron_numbers.pl
agat /usr/bin/vendor_perl/agat_sp_filter_gene_by_length.pl
agat /usr/bin/vendor_perl/agat_sp_filter_incomplete_gene_coding_models.pl
agat /usr/bin/vendor_perl/agat_sp_filter_record_by_coordinates.pl
agat /usr/bin/vendor_perl/agat_sp_fix_cds_phases.pl
agat /usr/bin/vendor_perl/agat_sp_fix_features_locations_duplicated.pl
agat /usr/bin/vendor_perl/agat_sp_fix_fusion.pl
agat /usr/bin/vendor_perl/agat_sp_fix_longest_ORF.pl
agat /usr/bin/vendor_perl/agat_sp_fix_overlaping_genes.pl
agat /usr/bin/vendor_perl/agat_sp_fix_small_exon_from_extremities.pl
agat /usr/bin/vendor_perl/agat_sp_flag_premature_stop_codons.pl
agat /usr/bin/vendor_perl/agat_sp_flag_short_introns.pl
agat /usr/bin/vendor_perl/agat_sp_functional_statistics.pl
agat /usr/bin/vendor_perl/agat_sp_keep_longest_isoform.pl
agat /usr/bin/vendor_perl/agat_sp_kraken_assess_liftover.pl
agat /usr/bin/vendor_perl/agat_sp_list_short_introns.pl
agat /usr/bin/vendor_perl/agat_sp_load_function_from_protein_align.pl
agat /usr/bin/vendor_perl/agat_sp_manage_IDs.pl
agat /usr/bin/vendor_perl/agat_sp_manage_UTRs.pl
agat /usr/bin/vendor_perl/agat_sp_manage_attributes.pl
agat /usr/bin/vendor_perl/agat_sp_manage_functional_annotation.pl
agat /usr/bin/vendor_perl/agat_sp_manage_introns.pl
agat /usr/bin/vendor_perl/agat_sp_merge_annotations.pl
agat /usr/bin/vendor_perl/agat_sp_move_attributes_within_records.pl
agat /usr/bin/vendor_perl/agat_sp_prokka_fix_fragmented_gene_annotations.pl
agat /usr/bin/vendor_perl/agat_sp_sensitivity_specificity.pl
agat /usr/bin/vendor_perl/agat_sp_separate_by_record_type.pl
agat /usr/bin/vendor_perl/agat_sp_statistics.pl
agat /usr/bin/vendor_perl/agat_sp_webApollo_compliant.pl
agat /usr/bin/vendor_perl/agat_sq_add_attributes_from_tsv.pl
agat /usr/bin/vendor_perl/agat_sq_add_hash_tag.pl
agat /usr/bin/vendor_perl/agat_sq_add_locus_tag.pl
agat /usr/bin/vendor_perl/agat_sq_count_attributes.pl
agat /usr/bin/vendor_perl/agat_sq_filter_feature_from_fasta.pl
agat /usr/bin/vendor_perl/agat_sq_list_attributes.pl
agat /usr/bin/vendor_perl/agat_sq_manage_IDs.pl
agat /usr/bin/vendor_perl/agat_sq_manage_attributes.pl
agat /usr/bin/vendor_perl/agat_sq_mask.pl
agat /usr/bin/vendor_perl/agat_sq_remove_redundant_entries.pl
agat /usr/bin/vendor_perl/agat_sq_rename_seqid.pl
agat /usr/bin/vendor_perl/agat_sq_repeats_analyzer.pl
agat /usr/bin/vendor_perl/agat_sq_reverse_complement.pl
agat /usr/bin/vendor_perl/agat_sq_rfam_analyzer.pl
agat /usr/bin/vendor_perl/agat_sq_split.pl
agat /usr/bin/vendor_perl/agat_sq_stat_basic.pl
agat /usr/share/
agat /usr/share/man/
agat /usr/share/man/man1/
agat /usr/share/man/man1/agat_convert_bed2gff.pl.1p.gz
agat /usr/share/man/man1/agat_convert_embl2gff.pl.1p.gz
agat /usr/share/man/man1/agat_convert_genscan2gff.pl.1p.gz
agat /usr/share/man/man1/agat_convert_mfannot2gff.pl.1p.gz
agat /usr/share/man/man1/agat_convert_minimap2_bam2gff.pl.1p.gz
agat /usr/share/man/man1/agat_convert_sp_gff2bed.pl.1p.gz
agat /usr/share/man/man1/agat_convert_sp_gff2gtf.pl.1p.gz
agat /usr/share/man/man1/agat_convert_sp_gff2tsv.pl.1p.gz
agat /usr/share/man/man1/agat_convert_sp_gff2zff.pl.1p.gz
agat /usr/share/man/man1/agat_convert_sp_gxf2gxf.pl.1p.gz
agat /usr/share/man/man1/agat_sp_Prokka_inferNameFromAttributes.pl.1p.gz
agat /usr/share/man/man1/agat_sp_add_attribute_shortest_exon_size.pl.1p.gz
agat /usr/share/man/man1/agat_sp_add_attribute_shortest_intron_size.pl.1p.gz
agat /usr/share/man/man1/agat_sp_add_intergenic_regions.pl.1p.gz
agat /usr/share/man/man1/agat_sp_add_introns.pl.1p.gz
agat /usr/share/man/man1/agat_sp_add_splice_sites.pl.1p.gz
agat /usr/share/man/man1/agat_sp_add_start_and_stop.pl.1p.gz
agat /usr/share/man/man1/agat_sp_alignment_output_style.pl.1p.gz
agat /usr/share/man/man1/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl.1p.gz
agat /usr/share/man/man1/agat_sp_compare_two_BUSCOs.pl.1p.gz
agat /usr/share/man/man1/agat_sp_compare_two_annotations.pl.1p.gz
agat /usr/share/man/man1/agat_sp_complement_annotations.pl.1p.gz
agat /usr/share/man/man1/agat_sp_ensembl_output_style.pl.1p.gz
agat /usr/share/man/man1/agat_sp_extract_attributes.pl.1p.gz
agat /usr/share/man/man1/agat_sp_extract_sequences.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_by_ORF_size.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_by_locus_distance.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_by_mrnaBlastValue.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_feature_by_attribute_presence.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_feature_by_attribute_value.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_feature_from_keep_list.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_feature_from_kill_list.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_gene_by_intron_numbers.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_gene_by_length.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_incomplete_gene_coding_models.pl.1p.gz
agat /usr/share/man/man1/agat_sp_filter_record_by_coordinates.pl.1p.gz
agat /usr/share/man/man1/agat_sp_fix_cds_phases.pl.1p.gz
agat /usr/share/man/man1/agat_sp_fix_features_locations_duplicated.pl.1p.gz
agat /usr/share/man/man1/agat_sp_fix_fusion.pl.1p.gz
agat /usr/share/man/man1/agat_sp_fix_longest_ORF.pl.1p.gz
agat /usr/share/man/man1/agat_sp_fix_overlaping_genes.pl.1p.gz
agat /usr/share/man/man1/agat_sp_fix_small_exon_from_extremities.pl.1p.gz
agat /usr/share/man/man1/agat_sp_flag_premature_stop_codons.pl.1p.gz
agat /usr/share/man/man1/agat_sp_flag_short_introns.pl.1p.gz
agat /usr/share/man/man1/agat_sp_functional_statistics.pl.1p.gz
agat /usr/share/man/man1/agat_sp_keep_longest_isoform.pl.1p.gz
agat /usr/share/man/man1/agat_sp_kraken_assess_liftover.pl.1p.gz
agat /usr/share/man/man1/agat_sp_list_short_introns.pl.1p.gz
agat /usr/share/man/man1/agat_sp_load_function_from_protein_align.pl.1p.gz
agat /usr/share/man/man1/agat_sp_manage_IDs.pl.1p.gz
agat /usr/share/man/man1/agat_sp_manage_UTRs.pl.1p.gz
agat /usr/share/man/man1/agat_sp_manage_attributes.pl.1p.gz
agat /usr/share/man/man1/agat_sp_manage_functional_annotation.pl.1p.gz
agat /usr/share/man/man1/agat_sp_manage_introns.pl.1p.gz
agat /usr/share/man/man1/agat_sp_merge_annotations.pl.1p.gz
agat /usr/share/man/man1/agat_sp_move_attributes_within_records.pl.1p.gz
agat /usr/share/man/man1/agat_sp_prokka_fix_fragmented_gene_annotations.pl.1p.gz
agat /usr/share/man/man1/agat_sp_sensitivity_specificity.pl.1p.gz
agat /usr/share/man/man1/agat_sp_separate_by_record_type.pl.1p.gz
agat /usr/share/man/man1/agat_sp_statistics.pl.1p.gz
agat /usr/share/man/man1/agat_sp_webApollo_compliant.pl.1p.gz
agat /usr/share/man/man1/agat_sq_add_attributes_from_tsv.pl.1p.gz
agat /usr/share/man/man1/agat_sq_add_hash_tag.pl.1p.gz
agat /usr/share/man/man1/agat_sq_add_locus_tag.pl.1p.gz
agat /usr/share/man/man1/agat_sq_count_attributes.pl.1p.gz
agat /usr/share/man/man1/agat_sq_filter_feature_from_fasta.pl.1p.gz
agat /usr/share/man/man1/agat_sq_list_attributes.pl.1p.gz
agat /usr/share/man/man1/agat_sq_manage_IDs.pl.1p.gz
agat /usr/share/man/man1/agat_sq_manage_attributes.pl.1p.gz
agat /usr/share/man/man1/agat_sq_mask.pl.1p.gz
agat /usr/share/man/man1/agat_sq_remove_redundant_entries.pl.1p.gz
agat /usr/share/man/man1/agat_sq_rename_seqid.pl.1p.gz
agat /usr/share/man/man1/agat_sq_repeats_analyzer.pl.1p.gz
agat /usr/share/man/man1/agat_sq_reverse_complement.pl.1p.gz
agat /usr/share/man/man1/agat_sq_rfam_analyzer.pl.1p.gz
agat /usr/share/man/man1/agat_sq_split.pl.1p.gz
agat /usr/share/man/man1/agat_sq_stat_basic.pl.1p.gz
agat /usr/share/man/man3/
agat /usr/share/man/man3/AGAT::AGAT.3pm.gz
agat /usr/share/man/man3/AGAT::BioperlGFF.3pm.gz
agat /usr/share/man/man3/AGAT::Config.3pm.gz
agat /usr/share/man/man3/AGAT::Levels.3pm.gz
agat /usr/share/man/man3/AGAT::OmniscientI.3pm.gz
agat /usr/share/man/man3/AGAT::OmniscientO.3pm.gz
agat /usr/share/man/man3/AGAT::OmniscientStat.3pm.gz
agat /usr/share/man/man3/AGAT::OmniscientTool.3pm.gz
agat /usr/share/man/man3/AGAT::PlotR.3pm.gz
agat /usr/share/man/man3/AGAT::Utilities.3pm.gz
agat /usr/share/perl5/
agat /usr/share/perl5/vendor_perl/
agat /usr/share/perl5/vendor_perl/AGAT/
agat /usr/share/perl5/vendor_perl/AGAT/AGAT.pm
agat /usr/share/perl5/vendor_perl/AGAT/AppEaser.pm
agat /usr/share/perl5/vendor_perl/AGAT/BioperlGFF.pm
agat /usr/share/perl5/vendor_perl/AGAT/Config.pm
agat /usr/share/perl5/vendor_perl/AGAT/Levels.pm
agat /usr/share/perl5/vendor_perl/AGAT/OmniscientI.pm
agat /usr/share/perl5/vendor_perl/AGAT/OmniscientO.pm
agat /usr/share/perl5/vendor_perl/AGAT/OmniscientStat.pm
agat /usr/share/perl5/vendor_perl/AGAT/OmniscientToGTF.pm
agat /usr/share/perl5/vendor_perl/AGAT/OmniscientTool.pm
agat /usr/share/perl5/vendor_perl/AGAT/PlotR.pm
agat /usr/share/perl5/vendor_perl/AGAT/Utilities.pm
agat /usr/share/perl5/vendor_perl/auto/
agat /usr/share/perl5/vendor_perl/auto/share/
agat /usr/share/perl5/vendor_perl/auto/share/dist/
agat /usr/share/perl5/vendor_perl/auto/share/dist/AGAT/
agat /usr/share/perl5/vendor_perl/auto/share/dist/AGAT/agat_config.yaml
agat /usr/share/perl5/vendor_perl/auto/share/dist/AGAT/feature_levels.yaml
agat /usr/share/perl5/vendor_perl/auto/share/dist/AGAT/so.obo please note i have built packages for using either path but the error still persists. |
Thank you @kbipinkumar for your help. |
Dear perl Master @viklund, |
Sorry for late reply. Yes, there seems to be something going on with the perl versions. Using the docker images of perl:5.34 and perl:5.36 and following the instructions in the repository, it succeeds for 5.34 but fails for 5.36. Check this dockerfile and just change the perl version and the build will fail for 5.36 but succeed for 5.34: From perl:5.36
RUN cpanm install BioPerl Graph::Directed LWP::UserAgent Carp Sort::Naturally File::Share File::ShareDir::Install Moose YAML LWP::Protocol::https Term::ProgressBar
RUN git clone https://github.com/NBISweden/AGAT.git
WORKDIR /usr/src/app/AGAT
RUN perl Makefile.PL
RUN make
RUN make test
RUN make install I don't know what to make of this right now. I might get some time to look into it more, I might not. But at least now it's easy to reproduce. |
@viklund Thank you for your feedback. |
Describe the bug
I am getting Undefined subroutine error messages after running agat_convert_sp_gff2gtf.pl.
General (please complete the following information):
To Reproduce
##I've tried this on a variety of different genomes as well, with the same issue. I'll also add this as an attachment.##
MPAO1_refseq_GCF_016107485.1.gff.gz
.gff downloaded from refseq: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016107485.1/
##input##
##I also tried running the line without the -o mpao1.gtf portion.##
agat_convert_sp_gff2gtf.pl --gff MPAO1_refseq_GCF_016107485.1.gff -o mpao1.gtf
##Output##
GTF version relax selected from the agat config file.
Undefined subroutine &main::prepare_gffout called at /usr/bin/vendor_perl/agat_convert_sp_gff2gtf.pl line 68.
##When I check line 68 it says the following. Admittedly, I am pretty new to perl, and I am not sure how to evaluate this line. I'll add this file as an attachment.)##
my $gffout = prepare_gffout($config, $opt_output);
agat_convert_sp_gff2gtf.pl.txt
Additional context
My issue is possibly related to #392. I have not yet tried a different Perl version, however. I will see if that works next.
Happy to provide other files/info, but I am not sure what would be helpful.
Thank you for your time!
The text was updated successfully, but these errors were encountered: