koadman/mauve

A genome alignment and visualization system

mauve's Issues

Futile gap opening

Hi,

When using progressiveMauve (default parameters), we often observe an issue I've call "futile gap opening". Here is an example:

ACTAGCTGATG--------CTGACGTAATCGTGATGATCGATGCTGA 
ACTAGCTGATGCTGACGTA--------ATCGTGATGATCGATGCTGA
ACTAGCTGATGCTGACGTA--------ATCGTGATGATCGATGCTGA

As you can see, these gaps are clearly not warranted.

The issue is quite common. The histogram below is from whole genome alignments. I won't describe the x-axis in detail but the sharp peak at 0.5 reflect these futile gap openings as a fraction of all gap events in the total alignment.

Does anyone know the nature of this issue and how to avoid?

Thanks.

(presumably) progressiveMauve uses out-dated .sslist file

While using progressiveMauve (build date 13 February 2015), I noticed that when I run mauve twice with the same fasta file path arguments, but with these fasta files having a bit different contents on the second run, mauve gave wrong results on the second run.
When I removed the .sslist file that mauve created on the first run, the second run gave good results.

So my guess is that I got wrong results on the second run (in case I didn't remove the .sslist file) because mauve saw the .sslist file that was generated on the first run and skipped generating it and just used it, even though it did not fit the new sequences, leading to wrong results.

(My workaround for this is to simply always delete the .sslist file (if it exists) before running progressiveMauve)

how to display locus in mauve

Hi,

I annotate bacterial genomes with bakta and I can modify the "locus name" to include, for example, the name of my bacterial strain. Is it possible to display the "locus name" at the "definition" location in the mauve software ?

Thanks for your help

Corentin

A bug in install of bactopia：assembly_qc-2.2.x and checkm_data_2015_01_16.tar.gz

Hi, I find a bug as follows:

(bactopia) ht@prp:~$ bactopia download --build_all --keep_file
2023-01-21 07:13:30:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details.
2023-01-21 07:13:30:root:INFO - Found /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/linux/assembly_qc.yml (3 of 6), begin build to /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x
External command failed with exit code 1!

Command:
bash -c 'mamba env create -f /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/linux/assembly_qc.yml --prefix /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x --force'

Standard output:
bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
Transaction

Prefix: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x

Updating specs:

• _libgcc_mutex=0.1
• _openmp_mutex=4.5
• alsa-lib=1.2.8
• bedtools=2.30.0
• blast=2.13.0
• brotli=1.0.9
• brotli-bin=1.0.9
• bwa=0.7.17
• bzip2=1.0.8
• c-ares=1.18.1
• ca-certificates=2022.9.24
• cairo=1.16.0
• certifi=2022.9.24
• checkm-genome=1.2.2
• circos=0.69.8
• contourpy=1.0.6
• coreutils=9.1
• curl=7.86.0
• cycler=0.11.0
• dendropy=4.5.2
• entrez-direct=16.2
• expat=2.5.0
• font-ttf-dejavu-sans-mono=2.37
• font-ttf-inconsolata=3.000
• font-ttf-source-code-pro=2.038
• font-ttf-ubuntu=0.83
• fontconfig=2.14.1
• fonts-conda-ecosystem=1
• fonts-conda-forge=1
• fonttools=4.38.0
• freetype=2.12.1
• gettext=0.21.1
• giflib=5.2.1
• glimmerhmm=3.0.4
• graphite2=1.3.13
• harfbuzz=5.3.0
• hmmer=3.3.2
• icu=70.1
• joblib=1.2.0
• jpeg=9e
• k8=0.2.5
• keyutils=1.6.1
• kiwisolver=1.4.4
• krb5=1.19.3
• lcms2=2.14
• ld_impl_linux-64=2.39
• lerc=4.0.0
• libblas=3.9.0
• libbrotlicommon=1.0.9
• libbrotlidec=1.0.9
• libbrotlienc=1.0.9
• libcblas=3.9.0
• libcups=2.3.3
• libcurl=7.86.0
• libdeflate=1.13
• libedit=3.1.20191231
• libev=4.33
• libffi=3.4.2
• libgcc-ng=12.2.0
• libgd=2.3.3
• libgfortran-ng=12.2.0
• libgfortran5=12.2.0
• libglib=2.74.1
• libgomp=12.2.0
• libiconv=1.17
• libidn2=2.3.4
• liblapack=3.9.0
• libnghttp2=1.47.0
• libnsl=2.0.0
• libopenblas=0.3.21
• libpng=1.6.38
• libsqlite=3.39.4
• libssh2=1.10.0
• libstdcxx-ng=12.2.0
• libtiff=4.4.0
• libunistring=0.9.10
• libuuid=2.32.1
• libwebp=1.2.4
• libwebp-base=1.2.4
• libxcb=1.13
• libzlib=1.2.13
• matplotlib-base=3.6.2
• minimap2=2.24
• munkres=1.1.4
• ncurses=6.3
• numpy=1.23.4
• openjdk=17.0.3
• openjpeg=2.5.0
• openssl=1.1.1s
• packaging=21.3
• pcre=8.45
• pcre2=10.40
• perl=5.32.1
• perl-archive-tar=2.40
• perl-b-cow=0.007
• perl-carp=1.50
• perl-clone=0.46
• perl-common-sense=3.75
• perl-compress-raw-bzip2=2.201
• perl-compress-raw-zlib=2.202
• perl-config-general=2.65
• perl-digest-perl-md5=1.9
• perl-encode=3.19
• perl-exporter=5.74
• perl-exporter-tiny=1.002002
• perl-extutils-config=0.008
• perl-extutils-helpers=0.026
• perl-extutils-installpaths=0.012
• perl-extutils-makemaker=7.64
• perl-extutils-pl2bat=0.005
• perl-font-ttf=1.06
• perl-gd=2.76
• perl-io-compress=2.201
• perl-io-string=1.08
• perl-io-zlib=1.11
• perl-json=4.10
• perl-json-xs=2.34
• perl-list-moreutils=0.430
• perl-list-moreutils-xs=0.430
• perl-math-bezier=0.01
• perl-math-round=0.07
• perl-math-vecstat=0.08
• perl-module-build-tiny=0.039
• perl-module-implementation=0.09
• perl-module-runtime=0.016
• perl-number-format=1.75
• perl-params-validate=1.31
• perl-parent=0.238
• perl-pathtools=3.75
• perl-readonly=2.05
• perl-regexp-common=2017060201
• perl-scalar-list-utils=1.63
• perl-set-intspan=1.19
• perl-statistics-basic=1.6611
• perl-storable=3.15
• perl-svg=2.87
• perl-test-fatal=0.016
• perl-text-format=0.62
• perl-time-hires=1.9764
• perl-try-tiny=0.31
• perl-types-serialiser=1.01
• perl-xml-parser=2.44_01
• pigz=2.6
• pillow=9.2.0
• pip=22.3.1
• pixman=0.40.0
• pplacer=1.1.alpha19
• prodigal=2.6.3
• pthread-stubs=0.4
• pyparsing=3.0.9
• pysam=0.19.1
• python=3.10.6
• python-dateutil=2.8.2
• python_abi=3.10
• quast=5.2.0
• readline=8.1.2
• scipy=1.9.3
• sed=4.8
• setuptools=65.5.1
• simplejson=3.18.0
• six=1.16.0
• tk=8.6.12
• tzdata=2022f
• unicodedata2=15.0.0
• wget=1.20.3
• wheel=0.38.4
• xorg-fixesproto=5.0
• xorg-inputproto=2.3.2
• xorg-kbproto=1.0.7
• xorg-libice=1.0.10
• xorg-libsm=1.2.3
• xorg-libx11=1.7.2
• xorg-libxau=1.0.9
• xorg-libxdmcp=1.1.3
• xorg-libxext=1.3.4
• xorg-libxfixes=5.0.3
• xorg-libxi=1.7.10
• xorg-libxrender=0.9.10
• xorg-libxtst=1.2.3
• xorg-recordproto=1.14.2
• xorg-renderproto=0.11.1
• xorg-xextproto=7.3.0
• xorg-xproto=7.0.31
• xz=5.2.6
• zlib=1.2.13
• zstd=1.5.2

Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────────

• _libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
• _openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached
• alsa-lib 1.2.8 h166bdaf_0 conda-forge/linux-64 Cached
• bedtools 2.30.0 h468198e_3 bioconda/linux-64 Cached
• blast 2.13.0 hf3cf87c_0 bioconda/linux-64 Cached
• brotli 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• brotli-bin 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• bwa 0.7.17 h7132678_9 bioconda/linux-64 Cached
• bzip2 1.0.8 h7f98852_4 conda-forge/linux-64 Cached
• c-ares 1.18.1 h7f98852_0 conda-forge/linux-64 Cached
• ca-certificates 2022.9.24 ha878542_0 conda-forge/linux-64 Cached
• cairo 1.16.0 ha61ee94_1014 conda-forge/linux-64 Cached
• certifi 2022.9.24 pyhd8ed1ab_0 conda-forge/noarch Cached
• checkm-genome 1.2.2 pyhdfd78af_1 bioconda/noarch Cached
• circos 0.69.8 hdfd78af_1 bioconda/noarch Cached
• contourpy 1.0.6 py310hbf28c38_0 conda-forge/linux-64 Cached
• coreutils 9.1 h166bdaf_0 conda-forge/linux-64 Cached
• curl 7.86.0 h7bff187_1 conda-forge/linux-64 Cached
• cycler 0.11.0 pyhd8ed1ab_0 conda-forge/noarch Cached
• dendropy 4.5.2 pyh3252c3a_0 bioconda/noarch Cached
• entrez-direct 16.2 he881be0_1 bioconda/linux-64 Cached
• expat 2.5.0 h27087fc_0 conda-forge/linux-64 Cached
• font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge/noarch Cached
• font-ttf-inconsolata 3.000 h77eed37_0 conda-forge/noarch Cached
• font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge/noarch Cached
• font-ttf-ubuntu 0.83 hab24e00_0 conda-forge/noarch Cached
• fontconfig 2.14.1 hc2a2eb6_0 conda-forge/linux-64 Cached
• fonts-conda-ecosystem 1 0 conda-forge/noarch Cached
• fonts-conda-forge 1 0 conda-forge/noarch Cached
• fonttools 4.38.0 py310h5764c6d_1 conda-forge/linux-64 Cached
• freetype 2.12.1 hca18f0e_0 conda-forge/linux-64 Cached
• gettext 0.21.1 h27087fc_0 conda-forge/linux-64 Cached
• giflib 5.2.1 h36c2ea0_2 conda-forge/linux-64 Cached
• glimmerhmm 3.0.4 pl5321h87f3376_5 bioconda/linux-64 Cached
• graphite2 1.3.13 h58526e2_1001 conda-forge/linux-64 Cached
• harfbuzz 5.3.0 h418a68e_0 conda-forge/linux-64 Cached
• hmmer 3.3.2 h87f3376_2 bioconda/linux-64 Cached
• icu 70.1 h27087fc_0 conda-forge/linux-64 Cached
• joblib 1.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
• jpeg 9e h166bdaf_2 conda-forge/linux-64 Cached
• k8 0.2.5 hd03093a_2 bioconda/linux-64 Cached
• keyutils 1.6.1 h166bdaf_0 conda-forge/linux-64 Cached
• kiwisolver 1.4.4 py310hbf28c38_1 conda-forge/linux-64 Cached
• krb5 1.19.3 h3790be6_0 conda-forge/linux-64 Cached
• lcms2 2.14 h6ed2654_0 conda-forge/linux-64 Cached
• ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge/linux-64 Cached
• lerc 4.0.0 h27087fc_0 conda-forge/linux-64 Cached
• libblas 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
• libbrotlicommon 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• libbrotlidec 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• libbrotlienc 1.0.9 h166bdaf_8 conda-forge/linux-64 Cached
• libcblas 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
• libcups 2.3.3 h3e49a29_2 conda-forge/linux-64 Cached
• libcurl 7.86.0 h7bff187_1 conda-forge/linux-64 Cached
• libdeflate 1.13 h166bdaf_0 conda-forge/linux-64 Cached
• libedit 3.1.20191231 he28a2e2_2 conda-forge/linux-64 Cached
• libev 4.33 h516909a_1 conda-forge/linux-64 Cached
• libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
• libgcc-ng 12.2.0 h65d4601_19 conda-forge/linux-64 Cached
• libgd 2.3.3 h18fbbfe_3 conda-forge/linux-64 Cached
• libgfortran-ng 12.2.0 h69a702a_19 conda-forge/linux-64 Cached
• libgfortran5 12.2.0 h337968e_19 conda-forge/linux-64 Cached
• libglib 2.74.1 h606061b_1 conda-forge/linux-64 Cached
• libgomp 12.2.0 h65d4601_19 conda-forge/linux-64 Cached
• libiconv 1.17 h166bdaf_0 conda-forge/linux-64 Cached
• libidn2 2.3.4 h166bdaf_0 conda-forge/linux-64 Cached
• liblapack 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
• libnghttp2 1.47.0 hdcd2b5c_1 conda-forge/linux-64 Cached
• libnsl 2.0.0 h7f98852_0 conda-forge/linux-64 Cached
• libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge/linux-64 Cached
• libpng 1.6.38 h753d276_0 conda-forge/linux-64 Cached
• libsqlite 3.39.4 h753d276_0 conda-forge/linux-64 Cached
• libssh2 1.10.0 haa6b8db_3 conda-forge/linux-64 Cached
• libstdcxx-ng 12.2.0 h46fd767_19 conda-forge/linux-64 Cached
• libtiff 4.4.0 h0e0dad5_3 conda-forge/linux-64 Cached
• libunistring 0.9.10 h7f98852_0 conda-forge/linux-64 Cached
• libuuid 2.32.1 h7f98852_1000 conda-forge/linux-64 Cached
• libwebp 1.2.4 h522a892_0 conda-forge/linux-64 Cached
• libwebp-base 1.2.4 h166bdaf_0 conda-forge/linux-64 Cached
• libxcb 1.13 h7f98852_1004 conda-forge/linux-64 Cached
• libzlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
• matplotlib-base 3.6.2 py310h8d5ebf3_0 conda-forge/linux-64 Cached
• minimap2 2.24 h7132678_1 bioconda/linux-64 Cached
• munkres 1.1.4 pyh9f0ad1d_0 conda-forge/noarch Cached
• ncurses 6.3 h27087fc_1 conda-forge/linux-64 Cached
• numpy 1.23.4 py310h53a5b5f_1 conda-forge/linux-64 Cached
• openjdk 17.0.3 hafdced1_4 conda-forge/linux-64 Cached
• openjpeg 2.5.0 h7d73246_1 conda-forge/linux-64 Cached
• openssl 1.1.1s h0b41bf4_1 conda-forge/linux-64 Cached
• packaging 21.3 pyhd8ed1ab_0 conda-forge/noarch Cached
• pcre 8.45 h9c3ff4c_0 conda-forge/linux-64 Cached
• pcre2 10.40 hc3806b6_0 conda-forge/linux-64 Cached
• perl 5.32.1 2_h7f98852_perl5 conda-forge/linux-64 Cached
• perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-b-cow 0.007 pl5321h166bdaf_0 conda-forge/linux-64 Cached
• perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-clone 0.46 pl5321hec16e2b_0 bioconda/linux-64 Cached
• perl-common-sense 3.75 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda/linux-64 Cached
• perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge/linux-64 Cached
• perl-config-general 2.65 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-constant 1.33 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-cpan-meta 2.150010 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-cpan-meta-requirements 2.140 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-cpan-meta-yaml 0.018 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-data-dumper 2.183 pl5321hec16e2b_1 bioconda/linux-64 Cached
• perl-digest-perl-md5 1.9 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-encode 3.19 pl5321hec16e2b_1 bioconda/linux-64 Cached
• perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-extutils-cbuilder 0.280230 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-extutils-config 0.008 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-extutils-helpers 0.026 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-extutils-installpaths 0.012 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-extutils-parsexs 3.44 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-extutils-pl2bat 0.005 pl5321ha770c72_0 conda-forge/linux-64 Cached
• perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-font-ttf 1.06 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-gd 2.76 pl5321h5b5514e_1 bioconda/linux-64 Cached
• perl-getopt-long 2.54 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-io-compress 2.201 pl5321h87f3376_0 bioconda/linux-64 Cached
• perl-io-string 1.08 pl5321hdfd78af_4 bioconda/noarch Cached
• perl-io-zlib 1.11 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-ipc-cmd 1.04 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-json 4.10 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-json-pp 4.11 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-json-xs 2.34 pl5321h9f5acd7_5 bioconda/linux-64 Cached
• perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-list-moreutils-xs 0.430 pl5321hec16e2b_1 bioconda/linux-64 Cached
• perl-locale-maketext-simple 0.21 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-math-bezier 0.01 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-math-round 0.07 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-math-vecstat 0.08 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-module-build-tiny 0.039 pl5321hdfd78af_5 bioconda/noarch Cached
• perl-module-corelist 5.20220620 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-module-implementation 0.09 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-module-load 0.34 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-module-load-conditional 0.68 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-module-metadata 1.000037 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-module-runtime 0.016 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-number-format 1.75 pl5321hdfd78af_4 bioconda/noarch Cached
• perl-params-check 0.38 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-params-validate 1.31 pl5321hec16e2b_0 bioconda/linux-64 Cached
• perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge/noarch Cached
• perl-pathtools 3.75 pl5321hec16e2b_3 bioconda/linux-64 Cached
• perl-perl-ostype 1.010 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-readonly 2.05 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-regexp-common 2017060201 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge/linux-64 Cached
• perl-set-intspan 1.19 pl5321hdfd78af_2 bioconda/noarch Cached
• perl-statistics-basic 1.6611 pl5321hdfd78af_3 bioconda/noarch Cached
• perl-storable 3.15 pl5321hec16e2b_3 bioconda/linux-64 Cached
• perl-svg 2.87 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-test-fatal 0.016 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-text-format 0.62 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-text-parsewords 3.31 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-time-hires 1.9764 pl5321hec16e2b_2 bioconda/linux-64 Cached
• perl-try-tiny 0.31 pl5321hdfd78af_1 bioconda/noarch Cached
• perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda/noarch Cached
• perl-version 0.9924 pl5321hec16e2b_2 bioconda/linux-64 Cached
• perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge/linux-64 Cached
• pigz 2.6 h27826a3_0 conda-forge/linux-64 Cached
• pillow 9.2.0 py310h454ad03_3 conda-forge/linux-64 Cached
• pip 22.3.1 pyhd8ed1ab_0 conda-forge/noarch Cached
• pixman 0.40.0 h36c2ea0_0 conda-forge/linux-64 Cached
• pplacer 1.1.alpha19 h9ee0642_2 bioconda/linux-64 Cached
• prodigal 2.6.3 hec16e2b_4 bioconda/linux-64 Cached
• pthread-stubs 0.4 h36c2ea0_1001 conda-forge/linux-64 Cached
• pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge/noarch Cached
• pysam 0.19.1 py310hff46b53_1 bioconda/linux-64 Cached
• python 3.10.6 h582c2e5_0_cpython conda-forge/linux-64 Cached
• python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached
• python_abi 3.10 3_cp310 conda-forge/linux-64 Cached
• quast 5.2.0 py310pl5321hc8f18ef_2 bioconda/linux-64 Cached
• readline 8.1.2 h0f457ee_0 conda-forge/linux-64 Cached
• scipy 1.9.3 py310hdfbd76f_2 conda-forge/linux-64 Cached
• sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
• setuptools 65.5.1 pyhd8ed1ab_0 conda-forge/noarch Cached
• simplejson 3.18.0 py310h5764c6d_0 conda-forge/linux-64 Cached
• six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached
• tk 8.6.12 h27826a3_0 conda-forge/linux-64 Cached
• tzdata 2022f h191b570_0 conda-forge/noarch Cached
• unicodedata2 15.0.0 py310h5764c6d_0 conda-forge/linux-64 Cached
• wget 1.20.3 ha56f1ee_1 conda-forge/linux-64 Cached
• wheel 0.38.4 pyhd8ed1ab_0 conda-forge/noarch Cached
• xorg-fixesproto 5.0 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-inputproto 2.3.2 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-kbproto 1.0.7 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-libice 1.0.10 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libsm 1.2.3 hd9c2040_1000 conda-forge/linux-64 Cached
• xorg-libx11 1.7.2 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxau 1.0.9 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxext 1.3.4 h7f98852_1 conda-forge/linux-64 Cached
• xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge/linux-64 Cached
• xorg-libxi 1.7.10 h7f98852_0 conda-forge/linux-64 Cached
• xorg-libxrender 0.9.10 h7f98852_1003 conda-forge/linux-64 Cached
• xorg-libxtst 1.2.3 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-recordproto 1.14.2 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-renderproto 0.11.1 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-xextproto 7.3.0 h7f98852_1002 conda-forge/linux-64 Cached
• xorg-xproto 7.0.31 h7f98852_1007 conda-forge/linux-64 Cached
• xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached
• zlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
• zstd 1.5.2 h3eb15da_6 conda-forge/linux-64 Cached

Summary:

Install: 207 packages

Total download: 0 B

────────────────────────────────────────────────────────────────────────────────────────────────────────

Looking for: ['_libgcc_mutex=0.1', '_openmp_mutex=4.5', 'alsa-lib=1.2.8', 'bedtools=2.30.0', 'blast=2.13.0', 'brotli=1.0.9', 'brotli-bin=1.0.9', 'bwa=0.7.17', 'bzip2=1.0.8', 'c-ares=1.18.1', 'ca-certificates=2022.9.24', 'cairo=1.16.0', 'certifi=2022.9.24', 'checkm-genome=1.2.2', 'circos=0.69.8', 'contourpy=1.0.6', 'coreutils=9.1', 'curl=7.86.0', 'cycler=0.11.0', 'dendropy=4.5.2', 'entrez-direct=16.2', 'expat=2.5.0', 'font-ttf-dejavu-sans-mono=2.37', 'font-ttf-inconsolata=3.000', 'font-ttf-source-code-pro=2.038', 'font-ttf-ubuntu=0.83', 'fontconfig=2.14.1', 'fonts-conda-ecosystem=1', 'fonts-conda-forge=1', 'fonttools=4.38.0', 'freetype=2.12.1', 'gettext=0.21.1', 'giflib=5.2.1', 'glimmerhmm=3.0.4', 'graphite2=1.3.13', 'harfbuzz=5.3.0', 'hmmer=3.3.2', 'icu=70.1', 'joblib=1.2.0', 'jpeg=9e', 'k8=0.2.5', 'keyutils=1.6.1', 'kiwisolver=1.4.4', 'krb5=1.19.3', 'lcms2=2.14', 'ld_impl_linux-64=2.39', 'lerc=4.0.0', 'libblas=3.9.0', 'libbrotlicommon=1.0.9', 'libbrotlidec=1.0.9', 'libbrotlienc=1.0.9', 'libcblas=3.9.0', 'libcups=2.3.3', 'libcurl=7.86.0', 'libdeflate=1.13', 'libedit=3.1.20191231', 'libev=4.33', 'libffi=3.4.2', 'libgcc-ng=12.2.0', 'libgd=2.3.3', 'libgfortran-ng=12.2.0', 'libgfortran5=12.2.0', 'libglib=2.74.1', 'libgomp=12.2.0', 'libiconv=1.17', 'libidn2=2.3.4', 'liblapack=3.9.0', 'libnghttp2=1.47.0', 'libnsl=2.0.0', 'libopenblas=0.3.21', 'libpng=1.6.38', 'libsqlite=3.39.4', 'libssh2=1.10.0', 'libstdcxx-ng=12.2.0', 'libtiff=4.4.0', 'libunistring=0.9.10', 'libuuid=2.32.1', 'libwebp=1.2.4', 'libwebp-base=1.2.4', 'libxcb=1.13', 'libzlib=1.2.13', 'matplotlib-base=3.6.2', 'minimap2=2.24', 'munkres=1.1.4', 'ncurses=6.3', 'numpy=1.23.4', 'openjdk=17.0.3', 'openjpeg=2.5.0', 'openssl=1.1.1s', 'packaging=21.3', 'pcre=8.45', 'pcre2=10.40', 'perl=5.32.1', 'perl-archive-tar=2.40', 'perl-b-cow=0.007', 'perl-carp=1.50', 'perl-clone=0.46', 'perl-common-sense=3.75', 'perl-compress-raw-bzip2=2.201', 'perl-compress-raw-zlib=2.202', 'perl-config-general=2.65', 'perl-digest-perl-md5=1.9', 'perl-encode=3.19', 'perl-exporter=5.74', 'perl-exporter-tiny=1.002002', 'perl-extutils-config=0.008', 'perl-extutils-helpers=0.026', 'perl-extutils-installpaths=0.012', 'perl-extutils-makemaker=7.64', 'perl-extutils-pl2bat=0.005', 'perl-font-ttf=1.06', 'perl-gd=2.76', 'perl-io-compress=2.201', 'perl-io-string=1.08', 'perl-io-zlib=1.11', 'perl-json=4.10', 'perl-json-xs=2.34', 'perl-list-moreutils=0.430', 'perl-list-moreutils-xs=0.430', 'perl-math-bezier=0.01', 'perl-math-round=0.07', 'perl-math-vecstat=0.08', 'perl-module-build-tiny=0.039', 'perl-module-implementation=0.09', 'perl-module-runtime=0.016', 'perl-number-format=1.75', 'perl-params-validate=1.31', 'perl-parent=0.238', 'perl-pathtools=3.75', 'perl-readonly=2.05', 'perl-regexp-common=2017060201', 'perl-scalar-list-utils=1.63', 'perl-set-intspan=1.19', 'perl-statistics-basic=1.6611', 'perl-storable=3.15', 'perl-svg=2.87', 'perl-test-fatal=0.016', 'perl-text-format=0.62', 'perl-time-hires=1.9764', 'perl-try-tiny=0.31', 'perl-types-serialiser=1.01', 'perl-xml-parser=2.44_01', 'pigz=2.6', 'pillow=9.2.0', 'pip=22.3.1', 'pixman=0.40.0', 'pplacer=1.1.alpha19', 'prodigal=2.6.3', 'pthread-stubs=0.4', 'pyparsing=3.0.9', 'pysam=0.19.1', 'python=3.10.6', 'python-dateutil=2.8.2', 'python_abi=3.10', 'quast=5.2.0', 'readline=8.1.2', 'scipy=1.9.3', 'sed=4.8', 'setuptools=65.5.1', 'simplejson=3.18.0', 'six=1.16.0', 'tk=8.6.12', 'tzdata=2022f', 'unicodedata2=15.0.0', 'wget=1.20.3', 'wheel=0.38.4', 'xorg-fixesproto=5.0', 'xorg-inputproto=2.3.2', 'xorg-kbproto=1.0.7', 'xorg-libice=1.0.10', 'xorg-libsm=1.2.3', 'xorg-libx11=1.7.2', 'xorg-libxau=1.0.9', 'xorg-libxdmcp=1.1.3', 'xorg-libxext=1.3.4', 'xorg-libxfixes=5.0.3', 'xorg-libxi=1.7.10', 'xorg-libxrender=0.9.10', 'xorg-libxtst=1.2.3', 'xorg-recordproto=1.14.2', 'xorg-renderproto=0.11.1', 'xorg-xextproto=7.3.0', 'xorg-xproto=7.0.31', 'xz=5.2.6', 'zlib=1.2.13', 'zstd=1.5.2']

Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... ERROR: post-link.sh was unable to download /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz with the sha256 971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c from https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz.

The default QUAST package does not include:

• GRIDSS (needed for structural variants detection)
• SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets)
• BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only!

To be able to use those, please run
quast-download-gridss
quast-download-silva
quast-download-busco

done
Rolling back transaction: ...working... done

Standard error:
ERROR conda.core.link:_execute(740): An error occurred while installing package 'bioconda::checkm-genome-1.2.2-pyhdfd78af_1'.

LinkError: post-link script failed for package bioconda::checkm-genome-1.2.2-pyhdfd78af_1
location of failed script: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/bin/.checkm-genome-post-link.sh
==> script messages <==
ERROR: post-link.sh was unable to download /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz with the sha256 971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c from https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz.

==> script output <==
stdout: /home/ht/anaconda3/envs/mamba/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x/staging/checkm_data_2015_01_16.tar.gz: FAILED

stderr: --2023-01-21 07:31:28-- https://zenodo.org/record/7401545/files/checkm_data_2015_01_16.tar.gz
Resolving zenodo.org (zenodo.org)... ::
Connecting to zenodo.org (zenodo.org)|::|:443... failed: Connection refused.
sha256sum: WARNING: 1 computed checksum did NOT match

return code: 1

()

Thanks

Haitao

install/java problem in Ubuntu 20.04

Hi

Im having a problem with 2.4.0, 2.3.1 and other installs on Ubuntu 20.04 using openjdk 11 or 14 and oracle 11

calling ./Mauve always returns:

Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "."
at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
at java.base/java.lang.Integer.parseInt(Integer.java:654)
at java.base/java.lang.Integer.parseInt(Integer.java:786)
at org.gel.mauve.gui.Mauve.hasRequiredJVM(Unknown Source)
at org.gel.mauve.gui.Mauve.init(Unknown Source)
at org.gel.mauve.gui.Mauve$2.run(Unknown Source)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:771)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:741)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

I cant seem to get around this - any ideas? I have messed around with the java path in the script - no differences. Am I missing some version or dependency?

best

Paul

Mauve Analyse Insertions and Deletions

I am trying to process the Mauve Alignment file for further analysis. It provides information about ranges of common subsequences :
1 1- 1000
2 1- 700

Apparently there are deletions in sequence 1, but how do I determine the positions of the deletions without a new alignment ?