For information: HmmCleaner.pl cannot be installed.

[theo-allnutt-bioinformatics]

It seems the current version of HmmCleaner.pl cannot be installed - the cpan testers log shows zero successes. I always get the error below where it asks for Bio::MUST:: Drivers and it freezes at t/exo_aligned.t ......... 1/? So far, no reply from author.

HmmCleaner.pl 5921.fna Can't locate Bio/MUST/Drivers.pm in @INC (you may need to install the Bio::MUST::Drivers module) (@INC contains: /g/data/if89/apps/perllib/v5.26.3/perl5/lib/BioPerl-1.6.924 /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/x86_64-linux-thread-multi /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5 /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/x86_64-linux-thread-multi /home/554/ta0341/perl5/lib/perl5/5.26.3/x86_64-linux-thread-multi /home/554/ta0341/perl5/lib/perl5/5.26.3 /home/554/ta0341/perl5/lib/perl5/x86_64-linux-thread-multi /home/554/ta0341/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/Bio/MUST/Apps/HmmCleaner.pm line 16. BEGIN failed--compilation aborted at /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/Bio/MUST/Apps/HmmCleaner.pm line 16. Compilation failed in require at /g/data/if89/apps/perllib/v5.26.3/perl5/bin/HmmCleaner.pl line 18. BEGIN failed--compilation aborted at /g/data/if89/apps/perllib/v5.26.3/perl5/bin/HmmCleaner.pl line 18.

when I try to install Bio:MUST:Drivers, or 'core' or anything, it stalls at the point below, after a day it does not change:

install Bio::MUST::Drivers Running install for module 'Bio::MUST::Drivers' Checksum for /home/554/ta0341/.cpan/sources/authors/id/D/DB/DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz ok Configuring D/DB/DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz with Makefile.PL Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::MUST::Drivers Writing MYMETA.yml and MYMETA.json DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz /half-root/usr/bin/perl Makefile.PL INSTALL_BASE=/home/554/ta0341/perl5/ -- OK Running make for D/DB/DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz cp lib/Bio/MUST/Drivers/Exonerate.pm blib/lib/Bio/MUST/Drivers/Exonerate.pm cp lib/Bio/MUST/Drivers/Blast/Database/Temporary.pm blib/lib/Bio/MUST/Drivers/Blast/Database/Temporary.pm cp lib/Bio/MUST/Drivers/Roles/Hmmerable.pm blib/lib/Bio/MUST/Drivers/Roles/Hmmerable.pm cp lib/Bio/MUST/Provision/ClustalO.pm blib/lib/Bio/MUST/Provision/ClustalO.pm cp lib/Bio/MUST/Drivers/Mafft.pm blib/lib/Bio/MUST/Drivers/Mafft.pm cp lib/Bio/MUST/Provision/Blast.pm blib/lib/Bio/MUST/Provision/Blast.pm cp lib/Bio/MUST/Provision/Mafft.pm blib/lib/Bio/MUST/Provision/Mafft.pm cp lib/Bio/MUST/Drivers/Exonerate/Aligned.pm blib/lib/Bio/MUST/Drivers/Exonerate/Aligned.pm cp lib/Bio/MUST/Drivers/Cap3.pm blib/lib/Bio/MUST/Drivers/Cap3.pm cp lib/Bio/MUST/Provision/Hmmer.pm blib/lib/Bio/MUST/Provision/Hmmer.pm cp lib/Bio/MUST/Provision/Exonerate.pm blib/lib/Bio/MUST/Provision/Exonerate.pm cp lib/Bio/MUST/Drivers/Roles/Blastable.pm blib/lib/Bio/MUST/Drivers/Roles/Blastable.pm cp lib/Bio/MUST/Drivers/Hmmer/Model/Database.pm blib/lib/Bio/MUST/Drivers/Hmmer/Model/Database.pm cp lib/Bio/MUST/Drivers/ClustalO.pm blib/lib/Bio/MUST/Drivers/ClustalO.pm cp lib/Bio/MUST/Drivers/Hmmer/Model.pm blib/lib/Bio/MUST/Drivers/Hmmer/Model.pm cp lib/Bio/MUST/Drivers/Exonerate/Sugar.pm blib/lib/Bio/MUST/Drivers/Exonerate/Sugar.pm cp lib/Bio/MUST/Drivers/Blast/Database.pm blib/lib/Bio/MUST/Drivers/Blast/Database.pm cp lib/Bio/MUST/Provision/CdHit.pm blib/lib/Bio/MUST/Provision/CdHit.pm cp lib/Bio/MUST/Drivers/Utils.pm blib/lib/Bio/MUST/Drivers/Utils.pm cp lib/Bio/MUST/Drivers/CdHit.pm blib/lib/Bio/MUST/Drivers/CdHit.pm cp lib/Bio/MUST/Drivers/Hmmer/Model/Temporary.pm blib/lib/Bio/MUST/Drivers/Hmmer/Model/Temporary.pm cp lib/Bio/MUST/Drivers/Blast.pm blib/lib/Bio/MUST/Drivers/Blast.pm cp lib/Bio/MUST/Drivers.pm blib/lib/Bio/MUST/Drivers.pm cp lib/Bio/MUST/Drivers/Hmmer.pm blib/lib/Bio/MUST/Drivers/Hmmer.pm cp lib/Bio/MUST/Provision/Cap3.pm blib/lib/Bio/MUST/Provision/Cap3.pm Manifying 25 pod documents DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz /bin/make -- OK Running make test PERL_DL_NONLAZY=1 "/half-root/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/.t t/author-critic.t ....... skipped: these tests are for testing by the author t/author-pod-syntax.t ... skipped: these tests are for testing by the author t/author-portability.t .. skipped: these tests are for testing by the author t/blast.t ............... 1/? [BMD] Warning: no valid -outfmt specified; defaulting to tabular! at t/blast.t line 52. t/blast.t ............... 7/? [BMD] Warning: no valid -outfmt specified; defaulting to tabular! at t/blast.t line 74. t/blast.t ............... ok t/cap3.t ................ ok t/cd_hit.t .............. ok t/clustalo.t ............ 1/? [BMD] Warning: align seqs before aligning on profile! at t/clustalo.t line 58. t/clustalo.t ............ ok t/exo_aligned.t ......... 1/?

[dongzhang0725]

Hi, I suggest you try the PhyloSuite virtual environment: https://dongzhang0725.github.io/installation/#4-Install-all-in-one-PhyloSuite-virtual-environment , I have installed all neccessary plugins in this environment, including Hmmcleaner.

Theo Allnutt Bioinformatics @.***> 于2023年4月24日周一 09:13写道：

It seems the current version of HmmCleaner.pl cannot be installed - the cpan testers log shows zero successes. I always get the error below where it asks for Bio::MUST:: Drivers and it freezes at t/exo_aligned.t ......... 1/? So far, no reply from author.

HmmCleaner.pl 5921.fna Can't locate Bio/MUST/Drivers.pm in @inc https://github.com/inc (you may need to install the Bio::MUST::Drivers module) @.*** https://github.com/inc contains: /g/data/if89/apps/perllib/v5.26.3/perl5/lib/BioPerl-1.6.924 /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/x86_64-linux-thread-multi /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5 /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/x86_64-linux-thread-multi /home/554/ta0341/perl5/lib/perl5/5.26.3/x86_64-linux-thread-multi /home/554/ta0341/perl5/lib/perl5/5.26.3 /home/554/ta0341/perl5/lib/perl5/x86_64-linux-thread-multi /home/554/ta0341/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/Bio/MUST/Apps/HmmCleaner.pm line 16. BEGIN failed--compilation aborted at /g/data/if89/apps/perllib/v5.26.3/perl5/lib/perl5/Bio/MUST/Apps/HmmCleaner.pm line 16. Compilation failed in require at /g/data/if89/apps/perllib/v5.26.3/perl5/bin/HmmCleaner.pl line 18. BEGIN failed--compilation aborted at /g/data/if89/apps/perllib/v5.26.3/perl5/bin/HmmCleaner.pl line 18.

when I try to install Bio:MUST:Drivers, or 'core' or anything, it stalls at the point below, after a day it does not change:

install Bio::MUST::Drivers Running install for module 'Bio::MUST::Drivers' Checksum for /home/554/ta0341/.cpan/sources/authors/id/D/DB/DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz ok Configuring D/DB/DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz with Makefile.PL Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::MUST::Drivers Writing MYMETA.yml and MYMETA.json DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz /half-root/usr/bin/perl Makefile.PL INSTALL_BASE=/home/554/ta0341/perl5/ -- OK Running make for D/DB/DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz cp lib/Bio/MUST/Drivers/Exonerate.pm blib/lib/Bio/MUST/Drivers/Exonerate.pm cp lib/Bio/MUST/Drivers/Blast/Database/Temporary.pm blib/lib/Bio/MUST/Drivers/Blast/Database/Temporary.pm cp lib/Bio/MUST/Drivers/Roles/Hmmerable.pm blib/lib/Bio/MUST/Drivers/Roles/Hmmerable.pm cp lib/Bio/MUST/Provision/ClustalO.pm blib/lib/Bio/MUST/Provision/ClustalO.pm cp lib/Bio/MUST/Drivers/Mafft.pm blib/lib/Bio/MUST/Drivers/Mafft.pm cp lib/Bio/MUST/Provision/Blast.pm blib/lib/Bio/MUST/Provision/Blast.pm cp lib/Bio/MUST/Provision/Mafft.pm blib/lib/Bio/MUST/Provision/Mafft.pm cp lib/Bio/MUST/Drivers/Exonerate/Aligned.pm blib/lib/Bio/MUST/Drivers/Exonerate/Aligned.pm cp lib/Bio/MUST/Drivers/Cap3.pm blib/lib/Bio/MUST/Drivers/Cap3.pm cp lib/Bio/MUST/Provision/Hmmer.pm blib/lib/Bio/MUST/Provision/Hmmer.pm cp lib/Bio/MUST/Provision/Exonerate.pm blib/lib/Bio/MUST/Provision/Exonerate.pm cp lib/Bio/MUST/Drivers/Roles/Blastable.pm blib/lib/Bio/MUST/Drivers/Roles/Blastable.pm cp lib/Bio/MUST/Drivers/Hmmer/Model/Database.pm blib/lib/Bio/MUST/Drivers/Hmmer/Model/Database.pm cp lib/Bio/MUST/Drivers/ClustalO.pm blib/lib/Bio/MUST/Drivers/ClustalO.pm cp lib/Bio/MUST/Drivers/Hmmer/Model.pm blib/lib/Bio/MUST/Drivers/Hmmer/Model.pm cp lib/Bio/MUST/Drivers/Exonerate/Sugar.pm blib/lib/Bio/MUST/Drivers/Exonerate/Sugar.pm cp lib/Bio/MUST/Drivers/Blast/Database.pm blib/lib/Bio/MUST/Drivers/Blast/Database.pm cp lib/Bio/MUST/Provision/CdHit.pm blib/lib/Bio/MUST/Provision/CdHit.pm cp lib/Bio/MUST/Drivers/Utils.pm blib/lib/Bio/MUST/Drivers/Utils.pm cp lib/Bio/MUST/Drivers/CdHit.pm blib/lib/Bio/MUST/Drivers/CdHit.pm cp lib/Bio/MUST/Drivers/Hmmer/Model/Temporary.pm blib/lib/Bio/MUST/Drivers/Hmmer/Model/Temporary.pm cp lib/Bio/MUST/Drivers/Blast.pm blib/lib/Bio/MUST/Drivers/Blast.pm cp lib/Bio/MUST/Drivers.pm blib/lib/Bio/MUST/Drivers.pm cp lib/Bio/MUST/Drivers/Hmmer.pm blib/lib/Bio/MUST/Drivers/Hmmer.pm cp lib/Bio/MUST/Provision/Cap3.pm blib/lib/Bio/MUST/Provision/Cap3.pm Manifying 25 pod documents DBAURAIN/Bio-MUST-Drivers-0.210160.tar.gz /bin/make -- OK Running make test PERL_DL_NONLAZY=1 "/half-root/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/.t t/author-critic.t ....... skipped: these tests are for testing by the author t/author-pod-syntax.t ... skipped: these tests are for testing by the author t/author-portability.t .. skipped: these tests are for testing by the author t/blast.t ............... 1/? [BMD] Warning: no valid -outfmt specified; defaulting to tabular! at t/blast.t line 52. t/blast.t ............... 7/? [BMD] Warning: no valid -outfmt specified; defaulting to tabular! at t/blast.t line 74. t/blast.t ............... ok t/cap3.t ................ ok t/cd_hit.t .............. ok t/clustalo.t ............ 1/? [BMD] Warning: align seqs before aligning on profile! at t/clustalo.t line 58. t/clustalo.t ............ ok t/exo_aligned.t ......... 1/?

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[theo-allnutt-bioinformatics]

Unfortunately, I cannot use docker or conda in my current HPC account.