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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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AGAT installation - "make test " shows two failed tests. #499

Closed Vijithkumar2020 closed 1 month ago

Vijithkumar2020 commented 1 month ago

The "make test" shows two failed tests. 

$ make test 
Skip blib/lib/auto/share/dist/AGAT/so.obo (unchanged)
Skip blib/lib/auto/share/dist/AGAT/agat_config.yaml (unchanged)
Skip blib/lib/auto/share/dist/AGAT/feature_levels.yaml (unchanged)
PERL_DL_NONLAZY=1 "/home/palmyra/anaconda3/envs/agat/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/config.t ........... ok   
t/gff_other.t ........ 5/8 
#   Failed test 'issue389 check'
#   at t/gff_other.t line 82.
t/gff_other.t ........ 8/8 # Looks like you failed 1 test of 8.
t/gff_other.t ........ Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/8 subtests 
t/gff_syntax.t ....... ok     
t/gff_version.t ...... ok   
t/level_missing.t .... ok     
t/scripts_compile.t .. ok     
t/scripts_output.t ... 37/84 
#   Failed test 'output bin/agat_sp_filter_feature_by_attribute_value.pl'
#   at t/scripts_output.t line 379.
t/scripts_output.t ... 83/84 # Looks like you failed 1 test of 84.
t/scripts_output.t ... Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/84 subtests 
t/unitest.t .......... ok     

Test Summary Report
-------------------
t/gff_other.t      (Wstat: 256 (exited 1) Tests: 8 Failed: 1)
  Failed test:  5
  Non-zero exit status: 1
t/scripts_output.t (Wstat: 256 (exited 1) Tests: 84 Failed: 1)
  Failed test:  38
  Non-zero exit status: 1
Files=8, Tests=254, 516 wallclock secs ( 2.72 usr  0.33 sys + 492.91 cusr 23.09 csys = 519.05 CPU)
Result: FAIL
Failed 2/8 test programs. 2/254 subtests failed.
make: *** [Makefile:1730: test_dynamic] Error 255
Juke34 commented 1 month ago

What AGAT version are you using? You can try to get more information using Perl -I lib/AGAT/ t/gff_other.t

I guess one dependency is missing.

Vijithkumar2020 commented 1 month ago

It shows

$ agat --version
v1.0.0

After running your command it shows: 

$ perl -I lib/AGAT/ t/gff_other.t
Global symbol "%Config" requires explicit package name (did you forget to declare "my %Config"?) at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/File/Copy.pm line 102.
Global symbol "%Config" requires explicit package name (did you forget to declare "my %Config"?) at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/File/Copy.pm line 102.
Global symbol "%Config" requires explicit package name (did you forget to declare "my %Config"?) at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/File/Copy.pm line 102.
Compilation failed in require at lib/AGAT/Config.pm line 8.
BEGIN failed--compilation aborted at lib/AGAT/Config.pm line 8.
Compilation failed in require at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test2/Util.pm line 8.
BEGIN failed--compilation aborted at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test2/Util.pm line 8.
Compilation failed in require at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test/Builder.pm line 17.
BEGIN failed--compilation aborted at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test/Builder.pm line 17.
Compilation failed in require at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test/Builder/Module.pm line 5.
BEGIN failed--compilation aborted at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test/Builder/Module.pm line 5.
Compilation failed in require at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test/More.pm line 22.
BEGIN failed--compilation aborted at /home/palmyra/anaconda3/envs/agat/lib/perl5/core_perl/Test/More.pm line 22.
Compilation failed in require at t/gff_other.t line 5.
BEGIN failed--compilation aborted at t/gff_other.t line 5.
Vijithkumar2020 commented 1 month ago

I installed dependencies using conda install perl-bioperl perl-clone perl-graph perl-lwp-simple perl-carp perl-sort-naturally perl-file-share perl-file-sharedir-install perl-moose perl-yaml perl-lwp-protocol-https perl-term-progressbar

Juke34 commented 1 month ago

What says the ‘make’ command ?

Vijithkumar2020 commented 1 month ago

make says: 

$ make
cp share/feature_levels.yaml blib/lib/auto/share/dist/AGAT/feature_levels.yaml
cp share/so.obo blib/lib/auto/share/dist/AGAT/so.obo
cp share/agat_config.yaml blib/lib/auto/share/dist/AGAT/agat_config.yaml
cp lib/AGAT/AGAT.pm blib/lib/AGAT/AGAT.pm
cp lib/AGAT/AppEaser.pm blib/lib/AGAT/AppEaser.pm
cp lib/AGAT/PlotR.pm blib/lib/AGAT/PlotR.pm
cp lib/AGAT/OmniscientTool.pm blib/lib/AGAT/OmniscientTool.pm
cp lib/AGAT/Config.pm blib/lib/AGAT/Config.pm
cp lib/AGAT/BioperlGFF.pm blib/lib/AGAT/BioperlGFF.pm
cp lib/AGAT/OmniscientStat.pm blib/lib/AGAT/OmniscientStat.pm
cp lib/AGAT/OmniscientO.pm blib/lib/AGAT/OmniscientO.pm
cp lib/AGAT/OmniscientToGTF.pm blib/lib/AGAT/OmniscientToGTF.pm
cp lib/AGAT/Utilities.pm blib/lib/AGAT/Utilities.pm
cp lib/AGAT/OmniscientI.pm blib/lib/AGAT/OmniscientI.pm
cp lib/AGAT/Levels.pm blib/lib/AGAT/Levels.pm
cp bin/agat blib/script/agat
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat
cp bin/agat_convert_bed2gff.pl blib/script/agat_convert_bed2gff.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_bed2gff.pl
cp bin/agat_convert_embl2gff.pl blib/script/agat_convert_embl2gff.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_embl2gff.pl
cp bin/agat_convert_genscan2gff.pl blib/script/agat_convert_genscan2gff.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_genscan2gff.pl
cp bin/agat_convert_mfannot2gff.pl blib/script/agat_convert_mfannot2gff.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_mfannot2gff.pl
cp bin/agat_convert_minimap2_bam2gff.pl blib/script/agat_convert_minimap2_bam2gff.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_minimap2_bam2gff.pl
cp bin/agat_convert_sp_gff2bed.pl blib/script/agat_convert_sp_gff2bed.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_sp_gff2bed.pl
cp bin/agat_convert_sp_gff2gtf.pl blib/script/agat_convert_sp_gff2gtf.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_sp_gff2gtf.pl
cp bin/agat_convert_sp_gff2tsv.pl blib/script/agat_convert_sp_gff2tsv.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_sp_gff2tsv.pl
cp bin/agat_convert_sp_gff2zff.pl blib/script/agat_convert_sp_gff2zff.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_sp_gff2zff.pl
cp bin/agat_convert_sp_gxf2gxf.pl blib/script/agat_convert_sp_gxf2gxf.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_convert_sp_gxf2gxf.pl
cp bin/agat_sp_Prokka_inferNameFromAttributes.pl blib/script/agat_sp_Prokka_inferNameFromAttributes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_Prokka_inferNameFromAttributes.pl
cp bin/agat_sp_add_attribute_shortest_exon_size.pl blib/script/agat_sp_add_attribute_shortest_exon_size.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_add_attribute_shortest_exon_size.pl
cp bin/agat_sp_add_attribute_shortest_intron_size.pl blib/script/agat_sp_add_attribute_shortest_intron_size.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_add_attribute_shortest_intron_size.pl
cp bin/agat_sp_add_intergenic_regions.pl blib/script/agat_sp_add_intergenic_regions.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_add_intergenic_regions.pl
cp bin/agat_sp_add_introns.pl blib/script/agat_sp_add_introns.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_add_introns.pl
cp bin/agat_sp_add_splice_sites.pl blib/script/agat_sp_add_splice_sites.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_add_splice_sites.pl
cp bin/agat_sp_add_start_and_stop.pl blib/script/agat_sp_add_start_and_stop.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_add_start_and_stop.pl
cp bin/agat_sp_alignment_output_style.pl blib/script/agat_sp_alignment_output_style.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_alignment_output_style.pl
cp bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl blib/script/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl
cp bin/agat_sp_compare_two_BUSCOs.pl blib/script/agat_sp_compare_two_BUSCOs.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_compare_two_BUSCOs.pl
cp bin/agat_sp_compare_two_annotations.pl blib/script/agat_sp_compare_two_annotations.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_compare_two_annotations.pl
cp bin/agat_sp_complement_annotations.pl blib/script/agat_sp_complement_annotations.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_complement_annotations.pl
cp bin/agat_sp_ensembl_output_style.pl blib/script/agat_sp_ensembl_output_style.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_ensembl_output_style.pl
cp bin/agat_sp_extract_attributes.pl blib/script/agat_sp_extract_attributes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_extract_attributes.pl
cp bin/agat_sp_extract_sequences.pl blib/script/agat_sp_extract_sequences.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_extract_sequences.pl
cp bin/agat_sp_filter_by_ORF_size.pl blib/script/agat_sp_filter_by_ORF_size.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_by_ORF_size.pl
cp bin/agat_sp_filter_by_locus_distance.pl blib/script/agat_sp_filter_by_locus_distance.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_by_locus_distance.pl
cp bin/agat_sp_filter_by_mrnaBlastValue.pl blib/script/agat_sp_filter_by_mrnaBlastValue.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_by_mrnaBlastValue.pl
cp bin/agat_sp_filter_feature_by_attribute_presence.pl blib/script/agat_sp_filter_feature_by_attribute_presence.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_feature_by_attribute_presence.pl
cp bin/agat_sp_filter_feature_by_attribute_value.pl blib/script/agat_sp_filter_feature_by_attribute_value.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_feature_by_attribute_value.pl
cp bin/agat_sp_filter_feature_from_keep_list.pl blib/script/agat_sp_filter_feature_from_keep_list.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_feature_from_keep_list.pl
cp bin/agat_sp_filter_feature_from_kill_list.pl blib/script/agat_sp_filter_feature_from_kill_list.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_feature_from_kill_list.pl
cp bin/agat_sp_filter_gene_by_intron_numbers.pl blib/script/agat_sp_filter_gene_by_intron_numbers.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_gene_by_intron_numbers.pl
cp bin/agat_sp_filter_gene_by_length.pl blib/script/agat_sp_filter_gene_by_length.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_gene_by_length.pl
cp bin/agat_sp_filter_incomplete_gene_coding_models.pl blib/script/agat_sp_filter_incomplete_gene_coding_models.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_incomplete_gene_coding_models.pl
cp bin/agat_sp_filter_record_by_coordinates.pl blib/script/agat_sp_filter_record_by_coordinates.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_filter_record_by_coordinates.pl
cp bin/agat_sp_fix_cds_phases.pl blib/script/agat_sp_fix_cds_phases.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_fix_cds_phases.pl
cp bin/agat_sp_fix_features_locations_duplicated.pl blib/script/agat_sp_fix_features_locations_duplicated.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_fix_features_locations_duplicated.pl
cp bin/agat_sp_fix_fusion.pl blib/script/agat_sp_fix_fusion.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_fix_fusion.pl
cp bin/agat_sp_fix_longest_ORF.pl blib/script/agat_sp_fix_longest_ORF.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_fix_longest_ORF.pl
cp bin/agat_sp_fix_overlaping_genes.pl blib/script/agat_sp_fix_overlaping_genes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_fix_overlaping_genes.pl
cp bin/agat_sp_fix_small_exon_from_extremities.pl blib/script/agat_sp_fix_small_exon_from_extremities.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_fix_small_exon_from_extremities.pl
cp bin/agat_sp_flag_premature_stop_codons.pl blib/script/agat_sp_flag_premature_stop_codons.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_flag_premature_stop_codons.pl
cp bin/agat_sp_flag_short_introns.pl blib/script/agat_sp_flag_short_introns.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_flag_short_introns.pl
cp bin/agat_sp_functional_statistics.pl blib/script/agat_sp_functional_statistics.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_functional_statistics.pl
cp bin/agat_sp_keep_longest_isoform.pl blib/script/agat_sp_keep_longest_isoform.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_keep_longest_isoform.pl
cp bin/agat_sp_kraken_assess_liftover.pl blib/script/agat_sp_kraken_assess_liftover.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_kraken_assess_liftover.pl
cp bin/agat_sp_list_short_introns.pl blib/script/agat_sp_list_short_introns.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_list_short_introns.pl
cp bin/agat_sp_load_function_from_protein_align.pl blib/script/agat_sp_load_function_from_protein_align.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_load_function_from_protein_align.pl
cp bin/agat_sp_manage_IDs.pl blib/script/agat_sp_manage_IDs.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_manage_IDs.pl
cp bin/agat_sp_manage_UTRs.pl blib/script/agat_sp_manage_UTRs.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_manage_UTRs.pl
cp bin/agat_sp_manage_attributes.pl blib/script/agat_sp_manage_attributes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_manage_attributes.pl
cp bin/agat_sp_manage_functional_annotation.pl blib/script/agat_sp_manage_functional_annotation.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_manage_functional_annotation.pl
cp bin/agat_sp_manage_introns.pl blib/script/agat_sp_manage_introns.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_manage_introns.pl
cp bin/agat_sp_merge_annotations.pl blib/script/agat_sp_merge_annotations.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_merge_annotations.pl
cp bin/agat_sp_move_attributes_within_records.pl blib/script/agat_sp_move_attributes_within_records.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_move_attributes_within_records.pl
cp bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl blib/script/agat_sp_prokka_fix_fragmented_gene_annotations.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_prokka_fix_fragmented_gene_annotations.pl
cp bin/agat_sp_sensitivity_specificity.pl blib/script/agat_sp_sensitivity_specificity.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_sensitivity_specificity.pl
cp bin/agat_sp_separate_by_record_type.pl blib/script/agat_sp_separate_by_record_type.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_separate_by_record_type.pl
cp bin/agat_sp_statistics.pl blib/script/agat_sp_statistics.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_statistics.pl
cp bin/agat_sp_webApollo_compliant.pl blib/script/agat_sp_webApollo_compliant.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sp_webApollo_compliant.pl
cp bin/agat_sq_add_attributes_from_tsv.pl blib/script/agat_sq_add_attributes_from_tsv.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_add_attributes_from_tsv.pl
cp bin/agat_sq_add_hash_tag.pl blib/script/agat_sq_add_hash_tag.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_add_hash_tag.pl
cp bin/agat_sq_add_locus_tag.pl blib/script/agat_sq_add_locus_tag.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_add_locus_tag.pl
cp bin/agat_sq_count_attributes.pl blib/script/agat_sq_count_attributes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_count_attributes.pl
cp bin/agat_sq_filter_feature_from_fasta.pl blib/script/agat_sq_filter_feature_from_fasta.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_filter_feature_from_fasta.pl
cp bin/agat_sq_list_attributes.pl blib/script/agat_sq_list_attributes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_list_attributes.pl
cp bin/agat_sq_manage_IDs.pl blib/script/agat_sq_manage_IDs.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_manage_IDs.pl
cp bin/agat_sq_manage_attributes.pl blib/script/agat_sq_manage_attributes.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_manage_attributes.pl
cp bin/agat_sq_mask.pl blib/script/agat_sq_mask.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_mask.pl
cp bin/agat_sq_remove_redundant_entries.pl blib/script/agat_sq_remove_redundant_entries.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_remove_redundant_entries.pl
cp bin/agat_sq_rename_seqid.pl blib/script/agat_sq_rename_seqid.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_rename_seqid.pl
cp bin/agat_sq_repeats_analyzer.pl blib/script/agat_sq_repeats_analyzer.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_repeats_analyzer.pl
cp bin/agat_sq_reverse_complement.pl blib/script/agat_sq_reverse_complement.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_reverse_complement.pl
cp bin/agat_sq_rfam_analyzer.pl blib/script/agat_sq_rfam_analyzer.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_rfam_analyzer.pl
cp bin/agat_sq_split.pl blib/script/agat_sq_split.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_split.pl
cp bin/agat_sq_stat_basic.pl blib/script/agat_sq_stat_basic.pl
"/home/palmyra/anaconda3/envs/agat/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/agat_sq_stat_basic.pl
Manifying 28 pod documents
Manifying 26 pod documents
Manifying 23 pod documents
Manifying 10 pod documents