Prokka tbl2asn error


#1

Hi,

When running Prokka, I get the error message:

Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y ‘Annotated using prokka 1.11 from http://www.vicbioinformatics.com’ -Z prokka_A108/A108.err -i prokka_A108/A108.fsa 2> /dev/null

According to the Prokka message boards (https://github.com/tseemann/prokka/issues/139) this is because you do not have the latest version of tbl2asn. Please could this be installed?

Best wishes,

Ben


#2

Hi Ben,

You should be able to brew reinstall tbl2asn to get an updated version and get around this stupid license problem.

brew is from the linuxbrew package manager that comes pre-installed on GVL. You can read the documentation here.


#3

Hi Matt,

I tried your suggestion and I got the following error message:

Error: SHA256 mismatch
Expected: 730d9bcf6d654e2395d19e529f01a4f670030633129ceea2dbf6e4850e42aa2a
Actual: a5de4c025d83f148a8c7da79521bdb1511fa1442c3bfa97bbd1e444124807197
Archive: /mnt/gvl/tmp/homebrew_cache/tbl2asn-24.9.gz
To retry an incomplete download, remove the file above.

Following suggestions I found online for this issue, I then ran
’brew cleanup && brew update’

And then re-ran ‘brew reinstall tbl2asn’ and I got the following error:

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

==> Downloading ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
Already downloaded: /mnt/gvl/tmp/homebrew_cache/tbl2asn-24.9.gz
Error: SHA256 mismatch
Expected: 730d9bcf6d654e2395d19e529f01a4f670030633129ceea2dbf6e4850e42aa2a
Actual: a5de4c025d83f148a8c7da79521bdb1511fa1442c3bfa97bbd1e444124807197
Archive: /mnt/gvl/tmp/homebrew_cache/tbl2asn-24.9.gz
To retry an incomplete download, remove the file above.

I seemed to make it worse! Any ideas?

Best wishes,

Ben


#4

It still looks like brew is trying to install the cached tbl2asn.

Try removing prokka completely:

brew remove prokka

Then manually clearing the cache:

rm -rf /mnt/gvl/tmp/homebrew_cache/*

Then updating the formula list:

brew update

Then reinstalling prokka:

brew install prokka

If any of these steps fail, stop and post the error message, don’t carry on!


#5

Hi Matt,

after the first step I get the following error:

ubuntu@evans:~$ brew remove prokka
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gdbm.rb:10:in `block in class:Gdbm
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:12:in `block in class:Boost
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/automake.rb:10:in `block in class:Automake
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/bzip2.rb:10:in `block in class:Bzip2
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/curl.rb:9:in `block in class:Curl
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman
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Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/zlib.rb:10:in `block in class:Zlib
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gsl.rb:13:in `block in class:Gsl
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/mummer.rb:11:in `block in class:Mummer
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/szip.rb:9:in `block in class:Szip
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:8:in `block in class:Python3
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gpatch.rb:10:in `block in class:Gpatch
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/jpeg.rb:9:in `block in class:Jpeg
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast
Please report this to the homebrew/science tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast
Please report this to the homebrew/science tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast
Please report this to the homebrew/science tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast
Please report this to the homebrew/science tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python.rb:9:in `block in class:Python
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/linuxbrew/homebrew-xorg/libxmu.rb:9:in `block in class:Libxmu
Please report this to the linuxbrew/xorg tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql
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Warning: Calling BottleSpecification.revision is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/autoconf.rb:10:in `block in class:Autoconf
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Warning: Calling BottleSpecification.revision is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/linuxbrew/homebrew-xorg/libxt.rb:10:in `block in class:Libxt
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gdk-pixbuf.rb:8:in `block in class:GdkPixbuf
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gobject-introspection.rb:9:in `block in class:GobjectIntrospection
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/linuxbrew/homebrew-xorg/libxi.rb:10:in `block in class:Libxi
Please report this to the linuxbrew/xorg tap!

Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre
Please report this to the homebrew/core tap!

Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre
Please report this to the homebrew/core tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/metaphlan.rb:13:in `block in class:Metaphlan
Please report this to the homebrew/science tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/bedtools.rb:14:in `block in class:Bedtools
Please report this to the homebrew/science tap!

Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/expat.rb:13:in `block in class:Expat
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/htslib.rb:12:in `block in class:Htslib
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/aragorn.rb:12:in `block in class:Aragorn
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/fasttree.rb:11:in `block in class:Fasttree
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/exonerate.rb:10:in `block in class:Exonerate
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit
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Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/jellyfish-1.1.rb:11:in `block in class:Jellyfish11
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Warning: Calling BottleSpecification.revision is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:11:in `block in class:Pango
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango
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Warning: Calling fails_with :llvm is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango
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Warning: Calling BottleSpecification.revision is deprecated!
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/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-dupes/zlib.rb:10:in `block in class:Zlib
Please report this to the homebrew/dupes tap!

Error: Refusing to uninstall /mnt/gvl/apps/linuxbrew/Cellar/prokka/HEAD
because it is required by nullarbor, which is currently installed.
You can override this and force removal with:
brew uninstall --ignore-dependencies prokka


#6

Woah! OK, new strategy…

Can you get

brew upgrade

to run successfully?


#7

No. A lot of stuff happened, but at the end it said:

glibc: gawk is required to build glibc.
Install gawk with your host package manager if you have sudo access.
sudo apt-get install gawk
sudo yum install gawk
Error: An unsatisfied requirement failed this build.


#8

Right, first of all - sorry about this. It is absolutely fixable though, and we’ll upgrade all of the software installed by brew, which should make everything much more consistent.

Stuff happening is good! Could you run:

sudo apt-get install gawk

to install system gawk, then:

brew upgrade

again, please?


#9

Hi Matt,

gawk installed no problem, but then when I tried ‘brew upgrade’ a few things happened but then I got the error message:

Error: Failure while executing: /mnt/gvl/apps/linuxbrew/Cellar/glibc/2.23/bin/ldd /mnt/gvl/apps/linuxbrew/Cellar/glibc/2.23/bin/gencat
Inconsistency detected by ld.so: get-dynamic-info.h: 143: elf_get_dynamic_info: Assertion `info[DT_RPATH] == NULL’ failed!

ldd: exited with unknown exit code (127)


#10

Okay - I think its time to cut our losses with this one and move you onto a new instance. We’ve just upgraded all of the brew software on GVL, and you’ll automatically get access to this on a new instance.

I’ll write out the steps that you can take to switch your instances over. The “old instance” is the one that you’re currently using, and the “new instance” is the one that you’ll start in step 1. It will help you orientate yourself if you call your new instance something distinct from your old one.

Preparation (browser based)

  1. Start a new GVL instance using https://bryn.climb.ac.uk

  2. Sign into the advanced interface (Horizon), find the volumes page on the left-hand side and identify any volumes that are attached to the old instance, disregarding any with “boot volume” anywhere in the Name column.

  3. Use the dropdown on the right hand side to select “Manage Attachments” and use the button to “Detach Volume” from the old instance.

  4. Use the same “Manage Attachments” button to attach the volume to the new instance.


Mounting your volume (SSH-based)

  1. SSH to your new instance (check its ip address at https://bryn.climb.ac.uk).

  2. Make a new directory to mount the volume that you’ve just attached to the new instance, remembering that you can call it whatever you like:

mkdir volume_data

  1. Mount the volume that you’ve just attached at the directory you’ve just made and make sure you can write to it:

sudo mount /dev/vdb1 volume_data
sudo chown -R ubuntu:ubuntu volume_data


Moving final data (SSH-based)

  1. SSH to your old instance

  2. From your old instance, ensure that you can SSH to your new instance (again, get your new instance ip address from https://bryn.climb.ac.uk). When asked if you trust the server you’re connecting to, type “yes” and hit enter:

ssh [new_instance_ip]

  1. Make a new directory to hold the data that you’re transferring from your old instance:

mkdir old_instance_data

  1. Disconnect from your new instance, to return to your old one. To do this, you can type exit and hit enter, or press Ctrl+d. Notice the instance name change at your command prompt to confirm that you’re back on your old instance.

  2. Now we actually move the data using rsync. Move to your home directory first:

cd

  1. Then rsync the files from your home directory to the newly-created directory on your new instance. The trailing slash at the end of this command is quite important:

rsync -avzP * [new_instance_ip]:/home/ubuntu/old_instance_data/


Tidying up

  1. SSH to your new instance, and check that the files in old_instance_data and volume_data are correct and as expected.

  2. When you’re happy that everything is as it should be, you can terminate the old instance using https://bryn.climb.ac.uk


If anything there isn’t clear or you have any questions at all, please reply and I’ll help you through it - don’t risk your data!


#11

Hi Matt,

One initial question - I have another user who I invited as a member of my group. Are they on a separate instance (and therefore will not be affected by this)? I’m guessing so as I don’t see their files on my instance.
Related to this, they will need the initial issue with Prokka sorted as well - should they post themselves about this?


#12

Hi Matt,

Just wondering if you knew the answer to my question above?


#13

Hi Ben,

Sorry about the delayed response - we’ve had a bunch to do on the underlying CLIMB system this week.

I’ve also held off replying because we’re very full at all sites, and this would’ve made it difficult for you to launch a new VM for you to transfer your data to. We’re working on this, and will put out some communication shortly with an update.

  1. Your VM is your VM. No-one else can see the files on it, and nothing you do to it affects anyone else’s VM.

  2. I’d encourage anyone still using a GVL 4.1 to move to GVL 4.2. It solves a multitude of issues with with software compilation, upgrading and installation.