Bio-Roary v3.10.0 Perl 5 v5.24.2 darwin-thread-multi-2level
- Status
- Fail
- From
- Nigel Horne
- Dist
-
Bio-Roary v3.10.0
- Platform
- Perl 5 v5.24.2 darwin-thread-multi-2level
- Date
- 2017-09-13 09:11:52
- ID
- 94f704a8-9863-11e7-858d-72298177e65f
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Andrew Page,
This is a computer-generated report for Bio-Roary-3.10.0
on perl 5.24.2, created by CPAN-Reporter-1.2018.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/sw/bin/make test':
PERL_DL_NONLAZY=1 "/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/bin/perl5.24.2" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Bio/Roary/*.t t/Bio/Roary/CommandLine/*.t t/Bio/Roary/External/*.t t/Bio/Roary/Output/*.t t/Bio/Roary/QC/*.t
# Failed test 'blastp in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'makeblastdb in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'mcl in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'mcxdeblast in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'bedtools in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'prank in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'parallel in PATH'
# at t/00_requires_external.t line 19.
# Failed test 'mafft in PATH'
# at t/00_requires_external.t line 19.
# Looks like you failed 8 tests of 8.
t/00_requires_external.t ................................
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/8 subtests
t/Bio/Roary/AccessoryBinaryFasta.t ...................... ok
Cant open file: _accessory_clusters.clstr# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 2.
t/Bio/Roary/AccessoryClustering.t .......................
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
t/Bio/Roary/AnalyseGroups.t ............................. ok
t/Bio/Roary/AnnotateGroups.t ............................ ok
t/Bio/Roary/AssemblyStatistics.t ........................ ok
t/Bio/Roary/ChunkFastaFile.t ............................ ok
t/Bio/Roary/CombinedProteome.t .......................... ok
# Failed test 'Actual output file exists example_annotation.gff.proteome.faa -t 1 t/data/example_annotation.gff'
# at t/lib/TestHelper.pm line 139.
# Failed test 'Actual and expected output match for '-t 1 t/data/example_annotation.gff''
# at t/lib/TestHelper.pm line 148.
# example_annotation.gff.proteome.faa absent
# Failed test 'Actual output file exists example_annotation.gff.proteome.faa t/data/example_annotation.gff'
# at t/lib/TestHelper.pm line 139.
# Failed test 'Actual and expected output match for 't/data/example_annotation.gff''
# at t/lib/TestHelper.pm line 148.
# example_annotation.gff.proteome.faa absent
# Looks like you failed 4 tests of 7.
t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ........
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/7 subtests
t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t .. ok
t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_1.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_2.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_3.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_1.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_2.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_3.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_1.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_2.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_3.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_1.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_2.gff.proteome.faa: No such file or directory
grep: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/XOqigChK28/query_3.gff.proteome.faa: No such file or directory
# Failed test 'Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.gff -t t/data/query_2.gff,t/data/query_3.gff''
# at t/lib/TestHelper.pm line 38.
# Structures begin differing at:
# $got->[1] = Does not exist
# $expected->[1] = ARRAY(0x7fe27ad63c90)
# Looks like you failed 1 test of 37.
t/Bio/Roary/CommandLine/QueryRoary.t ....................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/37 subtests
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/4GYjxlT2jw/genbank1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/4GYjxlT2jw/genbank2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/4GYjxlT2jw/genbank3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'Actual output file exists gene_presence_absence.csv -j Local -t 1 --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff'
# at /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/t/lib/TestHelper.pm line 249.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 3.
t/Bio/Roary/CommandLine/Roary.t .........................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 1/3 subtests
t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ............ ok
t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ............. ok
t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ....... ok
t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t .... ok
t/Bio/Roary/ContigsToGeneIDsFromGFF.t ................... ok
t/Bio/Roary/EmblGroups.t ................................ ok
t/Bio/Roary/External/Blastp.t ........................... ok
t/Bio/Roary/External/Cdhit.t ............................ ok
# Failed test 'Check for parallel'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 ERROR: Can't find required 'parallel' in your $PATH
#
# doesn't match:
# (?^:Looking for 'parallel' - found )
# as expected
# Failed test 'Check for blastp'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 ERROR: Can't find required 'blastp' in your $PATH
#
# doesn't match:
# (?^:Looking for 'blastp' - found )
# as expected
# Failed test 'Check for makeblastdb'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 ERROR: Can't find required 'makeblastdb' in your $PATH
#
# doesn't match:
# (?^:Looking for 'makeblastdb' - found )
# as expected
# Failed test 'Check for mcl'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 ERROR: Can't find required 'mcl' in your $PATH
#
# doesn't match:
# (?^:Looking for 'mcl' - found )
# as expected
# Failed test 'Check for bedtools'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 ERROR: Can't find required 'bedtools' in your $PATH
#
# doesn't match:
# (?^:Looking for 'bedtools' - found )
# as expected
# Failed test 'Check for prank'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 Optional tool 'prank' not found in your $PATH
#
# doesn't match:
# (?^:Looking for 'prank' - found )
# as expected
# Failed test 'Check for mafft'
# at t/Bio/Roary/External/CheckTools.t line 17.
# STDERR:
# 2017/09/13 05:11:34 ERROR: Can't find required 'mafft' in your $PATH
#
# doesn't match:
# (?^:Looking for 'mafft' - found )
# as expected
# Looks like you failed 7 tests of 13.
t/Bio/Roary/External/CheckTools.t .......................
Dubious, test returned 7 (wstat 1792, 0x700)
Failed 7/13 subtests
sh: mafft: command not found
# Failed test 'output for mafft matches'
# at t/Bio/Roary/External/Mafft.t line 39.
# +---+-----+---+-----------------------------------------------------------------------------+
# | |Got | |Expected |
# | Ln| | Ln| |
# +---+-----+---+-----------------------------------------------------------------------------+
# | | * 1|>1111#5_04506 *
# | | * 2|------------------------------------------------------------ *
# | | * 3|------------------------------------------------------------ *
# | | * 4|------------------------------------------------------------ *
# | | * 5|------------------------------------------------------------ *
# | | * 6|------------------------------------------------------------ *
# | | * 7|------------------------------------------------------------ *
# | | * 8|------------------------------------------------------------ *
# | | * 9|---------atggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 10|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 11|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 12|>1234_8#75_04759 *
# | | * 13|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 14|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 15|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 16|ctggattctttccggcgggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 17|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 18|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 19|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 20|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 21|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 22|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 23|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1_02853 *
# | | * 24|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 25|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 26|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 27|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 28|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 29|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 30|ttaatgttttcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 31|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 32|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 33|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 34|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_SL1344_v2_02736 *
# | | * 35|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 36|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 37|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 38|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 39|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 40|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 41|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 42|gatttacgtatggcaatcaccttacgggagctggatggcctgagctgtgaagagatagcg *
# | | * 43|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 44|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 45|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_D23580_v1_02783 *
# | | * 46|atgagcgagcagttaacggaccaggtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 47|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 48|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 49|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 50|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 51|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 52|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 53|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 54|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 55|attgataataaagttcaaccgcttatcaggcgttga *
# | | * 56|>Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_DT2_v1_02741 *
# | | * 57|atgagcgagcagttaacggac---gtcctggttgaacgggtccagaagggagatcagaaa *
# | | * 58|gcctttaacttactggtagtgcgctaccagcataaagtggcgagtctggtttcccgctat *
# | | * 59|gtgccatcgggcgacgttcccgatgtcgtacaggaatcatttattaaggcctatcgcgcg *
# | | * 60|ctggattctttccggggggatagtgctttttatacctggttgtatcgtattgcggtcaat *
# | | * 61|accgcgaagaactacctggttgcgcaggggcgtcgtccgccttccagtgatgtagacgcg *
# | | * 62|attgaagcagaaaactttgaaagcggcggcgcgctgaaagaaatttcgaaccctgagaac *
# | | * 63|ttaatgttgtcagaagaactgagacagatagttttccgaactattgagtccctcccggaa *
# | | * 64|gatttacgtatggcaatcaccttacgggagctggatggcctgagctatgaagagatagcg *
# | | * 65|gctatcatggattgtccggtggggacggtgcgttcacgtatcttccgggcgcgggaagct *
# | | * 66|attgataataaagttcaaccgcttatcaggcgttga *
# +---+-----+---+-----------------------------------------------------------------------------+
# Looks like you failed 1 test of 6.
t/Bio/Roary/External/Mafft.t ............................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/6 subtests
t/Bio/Roary/External/Makeblastdb.t ...................... ok
2017/09/13 05:11:35 Cannot find the mcxdeblast executable, please ensure its in your PATH
# Tests were run but no plan was declared and done_testing() was not seen.
t/Bio/Roary/External/Mcl.t ..............................
Dubious, test returned 254 (wstat 65024, 0xfe00)
All 5 subtests passed
# Failed test 'output file exists'
# at t/Bio/Roary/External/Prank.t line 33.
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 't/data/prank_input.fa.aln': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::SortFasta::_input_seqio /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/blib/lib/Bio/Roary/SortFasta.pm:27
STACK: Bio::Roary::SortFasta::sort_fasta /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/blib/lib/Bio/Roary/SortFasta.pm:68
STACK: t/Bio/Roary/External/Prank.t:38
-----------------------------------------------------------
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 5.
t/Bio/Roary/External/Prank.t ............................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 1/5 subtests
t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t ........... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/5BX9bH8jX2/example_annotation.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/5BX9bH8jX2/example_annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome 1 as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 30.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/5BX9bH8jX2/example_annotation.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/D58Hl6Zf5I/example_annotation_no_fasta_line.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/D58Hl6Zf5I/example_annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome 1 as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 44.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/D58Hl6Zf5I/example_annotation_2.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank1.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 64.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank1.gff.proteome.faa absent
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank2.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 64.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank2.gff.proteome.faa absent
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank3.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 64.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/6t2QDkloU5/genbank3.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_3.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_1.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 87.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_1.gff.proteome.faa absent
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_2.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 87.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_2.gff.proteome.faa absent
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_3.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 87.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/Y3qOFIdoMr/query_3.gff.proteome.faa absent
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/KUBqbnGIKb/annotation_1.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/KUBqbnGIKb/annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/KUBqbnGIKb/annotation_1.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 112.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/KUBqbnGIKb/annotation_1.gff.proteome.faa absent
# Failed test 'content of proteome /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/KUBqbnGIKb/annotation_2.gff.proteome.faa as expected'
# at t/Bio/Roary/ExtractProteomeFromGFFs.t line 112.
# /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/KUBqbnGIKb/annotation_2.gff.proteome.faa absent
# Looks like you failed 10 tests of 20.
t/Bio/Roary/ExtractProteomeFromGFFs.t ...................
Dubious, test returned 10 (wstat 2560, 0xa00)
Failed 10/20 subtests
t/Bio/Roary/FilterFullClusters.t ........................ ok
t/Bio/Roary/GeneNamesFromGFF.t .......................... ok
t/Bio/Roary/GroupLabels.t ............................... ok
t/Bio/Roary/GroupStatistics.t ........................... ok
t/Bio/Roary/InflateClusters.t ........................... ok
t/Bio/Roary/OrderGenes.t ................................ ok
t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t ... ok
t/Bio/Roary/Output/DifferenceBetweenSets.t .............. ok
t/Bio/Roary/Output/GroupsMultifastaProtein.t ............ ok
t/Bio/Roary/Output/GroupsMultifastas.t .................. ok
Attribute (fasta_file) does not pass the type constraint because: Validation failed for 'Str' with value undef at reader Bio::Roary::Output::GroupsMultifastaNucleotide::fasta_file (defined at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 29) line 15
Bio::Roary::Output::GroupsMultifastaNucleotide::fasta_file('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x7fe63f96af18)') called at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 43
Bio::Roary::Output::GroupsMultifastaNucleotide::_build__input_seqio('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x7fe63f96af18)') called at reader Bio::Roary::Output::GroupsMultifastaNucleotide::_input_seqio (defined at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 30) line 8
Bio::Roary::Output::GroupsMultifastaNucleotide::_input_seqio('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x7fe63f96af18)') called at lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm line 53
Bio::Roary::Output::GroupsMultifastaNucleotide::populate_files('Bio::Roary::Output::GroupsMultifastaNucleotide=HASH(0x7fe63f96af18)') called at lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm line 65
Bio::Roary::Output::GroupsMultifastasNucleotide::create_files('Bio::Roary::Output::GroupsMultifastasNucleotide=HASH(0x7fe64051eb80)') called at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 40
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 127 just after 3.
t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ........
Dubious, test returned 127 (wstat 32512, 0x7f00)
All 3 subtests passed
t/Bio/Roary/Output/NumberOfGroups.t ..................... ok
t/Bio/Roary/Output/QueryGroups.t ........................ ok
t/Bio/Roary/ParallelAllAgainstAllBlast.t ................ ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/uf7lvyc4Ho/example_annotation.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/uf7lvyc4Ho/example_annotation_2.gff.proteome.faa.intermediate.extracted.fa': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib/Bio/SeqIO.pm:435
STACK: Bio::Roary::ExtractProteomeFromGFF::_fastatranslate /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:145
STACK: Bio::Roary::ExtractProteomeFromGFF::_convert_nucleotide_to_protein /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:159
STACK: Bio::Roary::ExtractProteomeFromGFF::fasta_file /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/ExtractProteomeFromGFF.pm:29
STACK: Bio::Roary::CommandLine::ExtractProteomeFromGff::run /Users/hornenj/.cpan/build/Bio-Roary-3.10.0-2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm:90
STACK: ./bin/extract_proteome_from_gff:14
-----------------------------------------------------------
t/Bio/Roary/PrepareInputFiles.t ......................... ok
t/Bio/Roary/PresenceAbsenceMatrix.t ..................... ok
t/Bio/Roary/QC/Report.t ................................. ok
2017/09/13 05:11:49 Input file contains duplicate gene IDs, attempting to fix by adding a unique suffix, new GFF in the fixed_input_files directory: t/data/reformat_input_gffs/query_2.gff
2017/09/13 05:11:49 Input file contains duplicate gene IDs, attempting to fix by adding a unique suffix, new GFF in the fixed_input_files directory: t/data/reformat_input_gffs/query_2.gff
t/Bio/Roary/ReformatInputGFFs.t ......................... ok
t/Bio/Roary/ReorderSpreadsheet.t ........................ ok
t/Bio/Roary/SampleOrder.t ............................... ok
t/Bio/Roary/SequenceLengths.t ........................... ok
t/Bio/Roary/SortFasta.t ................................. ok
t/Bio/Roary/SplitGroups.t ............................... ok
t/Bio/Roary/UniqueGenesPerSample.t ...................... ok
Test Summary Report
-------------------
t/00_requires_external.t (Wstat: 2048 Tests: 8 Failed: 8)
Failed tests: 1-8
Non-zero exit status: 8
t/Bio/Roary/AccessoryClustering.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t (Wstat: 1024 Tests: 7 Failed: 4)
Failed tests: 4-7
Non-zero exit status: 4
t/Bio/Roary/CommandLine/QueryRoary.t (Wstat: 256 Tests: 37 Failed: 1)
Failed test: 27
Non-zero exit status: 1
t/Bio/Roary/CommandLine/Roary.t (Wstat: 512 Tests: 3 Failed: 1)
Failed test: 3
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Bio/Roary/External/CheckTools.t (Wstat: 1792 Tests: 13 Failed: 7)
Failed tests: 3-9
Non-zero exit status: 7
t/Bio/Roary/External/Mafft.t (Wstat: 256 Tests: 6 Failed: 1)
Failed test: 6
Non-zero exit status: 1
t/Bio/Roary/External/Mcl.t (Wstat: 65024 Tests: 5 Failed: 0)
Non-zero exit status: 254
Parse errors: No plan found in TAP output
t/Bio/Roary/External/Prank.t (Wstat: 512 Tests: 5 Failed: 1)
Failed test: 5
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/Bio/Roary/ExtractProteomeFromGFFs.t (Wstat: 2560 Tests: 20 Failed: 10)
Failed tests: 4, 6, 9-11, 14-16, 19-20
Non-zero exit status: 10
t/Bio/Roary/Output/GroupsMultifastasNucleotide.t (Wstat: 32512 Tests: 3 Failed: 0)
Non-zero exit status: 127
Parse errors: No plan found in TAP output
Files=52, Tests=675, 31 wallclock secs ( 0.16 usr 0.10 sys + 22.16 cusr 9.04 csys = 31.46 CPU)
Result: FAIL
Failed 11/52 test programs. 33/675 subtests failed.
make: *** [Makefile:1393: test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------- ---- --------
Array::Utils 0 0.5
Bio::Perl 0 1.007002
Bio::SeqIO 0 0
Bio::Tools::GFF 0 1.007002
Bio::TreeIO 0 0
Cwd 0 3.63_01
Digest::MD5::File 0 0.08
Exception::Class 0 1.43
File::Basename 0 2.85
File::Copy 0 2.31
File::Find::Rule 0 0.34
File::Grep 0 0.02
File::Path 0 2.12_01
File::Slurper 0 0.009
File::Spec 0 3.63_01
File::Temp 0 0.2304
File::Which 0 1.21
FindBin 0 1.51
Getopt::Long 0 2.48
Graph 0 0.9704
Graph::Writer::Dot 0 2.09
List::Util 0 1.48
Log::Log4perl 0 1.49
Moose 0 2.2006
Moose::Role 0 2.2006
PerlIO::utf8_strict 0 0.007
POSIX 0 1.65
strict 0 1.11
Text::CSV 0 1.95
warnings 0 1.36
build_requires:
Module Need Have
------------------- ---- --------
Data::Dumper 0 2.160
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.30
Test::Files 0 0.14
Test::Most 0 0.35
Test::Output 0 1.031
configure_requires:
Module Need Have
------------------- ---- --------
ExtUtils::MakeMaker 0 7.30
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LC_ALL = POSIX
LDFLAGS =
PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/bin:/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/bin:/usr/bin:/bin:/usr/X11R6/bin
PERL5LIB = /Users/hornenj/.cpan/build/Text-CSV-1.95-7/blib/arch:/Users/hornenj/.cpan/build/Text-CSV-1.95-7/blib/lib:/Users/hornenj/.cpan/build/Test-Files-0.14-8/blib/arch:/Users/hornenj/.cpan/build/Test-Files-0.14-8/blib/lib:/Users/hornenj/.cpan/build/PerlIO-utf8_strict-0.007-14/blib/arch:/Users/hornenj/.cpan/build/PerlIO-utf8_strict-0.007-14/blib/lib:/Users/hornenj/.cpan/build/Graph-ReadWrite-2.09-6/blib/arch:/Users/hornenj/.cpan/build/Graph-ReadWrite-2.09-6/blib/lib:/Users/hornenj/.cpan/build/XML-Writer-0.625-6/blib/arch:/Users/hornenj/.cpan/build/XML-Writer-0.625-6/blib/lib:/Users/hornenj/.cpan/build/XML-Parser-2.44-13/blib/arch:/Users/hornenj/.cpan/build/XML-Parser-2.44-13/blib/lib:/Users/hornenj/.cpan/build/Parse-Yapp-1.21-8/blib/arch:/Users/hornenj/.cpan/build/Parse-Yapp-1.21-8/blib/lib:/Users/hornenj/.cpan/build/Graph-0.9704-6/blib/arch:/Users/hornenj/.cpan/build/Graph-0.9704-6/blib/lib:/Users/hornenj/.cpan/build/File-Slurper-0.009-26/blib/arch:/Users/hornenj/.cpan/build/File-Slurper-0.009-26/blib/lib:/Users/hornenj/.cpan/build/File-Grep-0.02-6/blib/arch:/Users/hornenj/.cpan/build/File-Grep-0.02-6/blib/lib:/Users/hornenj/.cpan/build/Env-Path-0.19-8/blib/arch:/Users/hornenj/.cpan/build/Env-Path-0.19-8/blib/lib:/Users/hornenj/.cpan/build/Digest-MD5-File-0.08-6/blib/arch:/Users/hornenj/.cpan/build/Digest-MD5-File-0.08-6/blib/lib:/Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-10/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-10/blib/lib:/Users/hornenj/.cpan/build/Array-Utils-0.5-7/blib/arch:/Users/hornenj/.cpan/build/Array-Utils-0.5-7/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 69618
PERL5_CPAN_IS_RUNNING = 69618
PERL5_MINISMOKEBOX = 0.68
PERLBREW_BASHRC_VERSION = 0.80
PERLBREW_HOME = /Users/hornenj/.perlbrew
PERLBREW_LIB =
PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/man
PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/bin
PERLBREW_PERL = perl-5.24.2
PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
PERLBREW_VERSION = 0.80
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_LOCAL_LIB_ROOT =
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm-256color
TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/bin/perl5.24.2
$UID/$EUID = 12481 / 12481
$GID = 14 14 5344 37191 527 12 62 204 399 206 37223 241 223
$EGID = 14 14 5344 37191 527 12 62 204 399 206 37223 241 223
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.16
CPAN::Meta 2.150005
Cwd 3.63_01
ExtUtils::CBuilder 0.280225
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.31
File::Spec 3.63_01
JSON 2.94
JSON::PP 2.27300_01
Module::Build 0.4224
Module::Signature n/a
Parse::CPAN::Meta 1.4417_001
Test::Harness 3.36_01
Test::More 1.302086
YAML 1.23
YAML::Syck 1.30
version 0.9916
--
Summary of my perl5 (revision 5 version 24 subversion 2) configuration:
Platform:
osname=darwin, osvers=15.6.0, archname=darwin-thread-multi-2level
uname='darwin ncbimac2027 15.6.0 darwin kernel version 15.6.0: fri feb 17 10:21:18 pst 2017; root:xnu-3248.60.11.4.1~1release_x86_64 x86_64 '
config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags=-O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -fomit-frame-pointer -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -ftree-vectorize -mmmx -msse -mfpmath=sse -msse2 -msse3 -msse4.1 -msse4.2 -fdiagnostics-color=auto -mtune=native -march=native -I/Users/hornenj/openssl/include -Acc=cc -Aeval:scriptdir=/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc=' cc', ccflags ='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -fomit-frame-pointer -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -ftree-vectorize -mmmx -msse -mfpmath=sse -msse2 -msse3 -msse4.1 -msse4.2 -fdiagnostics-color=auto -mtune=native -march=native -I/Users/hornenj/openssl/include -fno-strict-aliasing -fstack-protector-strong -I/usr/local/include',
optimize='-O3',
cppflags='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -fomit-frame-pointer -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -ftree-vectorize -mmmx -msse -mfpmath=sse -msse2 -msse3 -msse4.1 -msse4.2 -fdiagnostics-color=auto -mtune=native -march=native -I/Users/hornenj/openssl/include -fno-strict-aliasing -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678, doublekind=3
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16, longdblkind=3
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags =' -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/local/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib /usr/lib
libs=-lpthread -ldbm -ldl -lm -lutil -lc
perllibs=-lpthread -ldl -lm -lutil -lc
libc=, so=dylib, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_COPY_ON_WRITE PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_USE_DEVEL USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO
USE_PERL_ATOF USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.30
Built under darwin
Compiled at Jul 17 2017 12:57:09
%ENV:
PERL5LIB="/Users/hornenj/.cpan/build/Text-CSV-1.95-7/blib/arch:/Users/hornenj/.cpan/build/Text-CSV-1.95-7/blib/lib:/Users/hornenj/.cpan/build/Test-Files-0.14-8/blib/arch:/Users/hornenj/.cpan/build/Test-Files-0.14-8/blib/lib:/Users/hornenj/.cpan/build/PerlIO-utf8_strict-0.007-14/blib/arch:/Users/hornenj/.cpan/build/PerlIO-utf8_strict-0.007-14/blib/lib:/Users/hornenj/.cpan/build/Graph-ReadWrite-2.09-6/blib/arch:/Users/hornenj/.cpan/build/Graph-ReadWrite-2.09-6/blib/lib:/Users/hornenj/.cpan/build/XML-Writer-0.625-6/blib/arch:/Users/hornenj/.cpan/build/XML-Writer-0.625-6/blib/lib:/Users/hornenj/.cpan/build/XML-Parser-2.44-13/blib/arch:/Users/hornenj/.cpan/build/XML-Parser-2.44-13/blib/lib:/Users/hornenj/.cpan/build/Parse-Yapp-1.21-8/blib/arch:/Users/hornenj/.cpan/build/Parse-Yapp-1.21-8/blib/lib:/Users/hornenj/.cpan/build/Graph-0.9704-6/blib/arch:/Users/hornenj/.cpan/build/Graph-0.9704-6/blib/lib:/Users/hornenj/.cpan/build/File-Slurper-0.009-26/blib/arch:/Users/hornenj/.cpan/build/File-Slurper-0.009-26/blib/lib:/Users/hornenj/.cpan/build/File-Grep-0.02-6/blib/arch:/Users/hornenj/.cpan/build/File-Grep-0.02-6/blib/lib:/Users/hornenj/.cpan/build/Env-Path-0.19-8/blib/arch:/Users/hornenj/.cpan/build/Env-Path-0.19-8/blib/lib:/Users/hornenj/.cpan/build/Digest-MD5-File-0.08-6/blib/arch:/Users/hornenj/.cpan/build/Digest-MD5-File-0.08-6/blib/lib:/Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-10/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-10/blib/lib:/Users/hornenj/.cpan/build/Array-Utils-0.5-7/blib/arch:/Users/hornenj/.cpan/build/Array-Utils-0.5-7/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="69618"
PERL5_CPAN_IS_RUNNING="69618"
PERL5_MINISMOKEBOX="0.68"
PERLBREW_BASHRC_VERSION="0.80"
PERLBREW_HOME="/Users/hornenj/.perlbrew"
PERLBREW_LIB=""
PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/man"
PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/bin"
PERLBREW_PERL="perl-5.24.2"
PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
PERLBREW_VERSION="0.80"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_LOCAL_LIB_ROOT=""
PERL_MM_USE_DEFAULT="1"
@INC:
/Users/hornenj/.cpan/build/Text-CSV-1.95-7/blib/arch
/Users/hornenj/.cpan/build/Text-CSV-1.95-7/blib/lib
/Users/hornenj/.cpan/build/Test-Files-0.14-8/blib/arch
/Users/hornenj/.cpan/build/Test-Files-0.14-8/blib/lib
/Users/hornenj/.cpan/build/PerlIO-utf8_strict-0.007-14/blib/arch
/Users/hornenj/.cpan/build/PerlIO-utf8_strict-0.007-14/blib/lib
/Users/hornenj/.cpan/build/Graph-ReadWrite-2.09-6/blib/arch
/Users/hornenj/.cpan/build/Graph-ReadWrite-2.09-6/blib/lib
/Users/hornenj/.cpan/build/XML-Writer-0.625-6/blib/arch
/Users/hornenj/.cpan/build/XML-Writer-0.625-6/blib/lib
/Users/hornenj/.cpan/build/XML-Parser-2.44-13/blib/arch
/Users/hornenj/.cpan/build/XML-Parser-2.44-13/blib/lib
/Users/hornenj/.cpan/build/Parse-Yapp-1.21-8/blib/arch
/Users/hornenj/.cpan/build/Parse-Yapp-1.21-8/blib/lib
/Users/hornenj/.cpan/build/Graph-0.9704-6/blib/arch
/Users/hornenj/.cpan/build/Graph-0.9704-6/blib/lib
/Users/hornenj/.cpan/build/File-Slurper-0.009-26/blib/arch
/Users/hornenj/.cpan/build/File-Slurper-0.009-26/blib/lib
/Users/hornenj/.cpan/build/File-Grep-0.02-6/blib/arch
/Users/hornenj/.cpan/build/File-Grep-0.02-6/blib/lib
/Users/hornenj/.cpan/build/Env-Path-0.19-8/blib/arch
/Users/hornenj/.cpan/build/Env-Path-0.19-8/blib/lib
/Users/hornenj/.cpan/build/Digest-MD5-File-0.08-6/blib/arch
/Users/hornenj/.cpan/build/Digest-MD5-File-0.08-6/blib/lib
/Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/arch
/Users/hornenj/.cpan/build/BioPerl-1.007002-10/blib/lib
/Users/hornenj/.cpan/build/Data-Stag-0.14-10/blib/arch
/Users/hornenj/.cpan/build/Data-Stag-0.14-10/blib/lib
/Users/hornenj/.cpan/build/Array-Utils-0.5-7/blib/arch
/Users/hornenj/.cpan/build/Array-Utils-0.5-7/blib/lib
/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/lib/site_perl/5.24.2/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/lib/site_perl/5.24.2
/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/lib/5.24.2/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.24.2/lib/5.24.2
.