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lgpdevtools / sraX

Systematic resistome analysis
GNU General Public License v3.0
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sraX - no plots generated #4

Closed gaworj closed 3 years ago

gaworj commented 3 years ago

Hi,

First of all thank you very much for such amazing tool! I have installed SraX using conda and plots are not generated. After inspecting log files I have noticed that R packages are not installed so they were installed also via conda. Unfortunately the problem persist. Please have a look:

The creation of summary files finished at: Time: 23:21 hs | Date: 2021-10-19

The creation of HTML files plus embedded summary plots started at: Time: 23:21 hs | Date: 2021-10-19

Error in position_fill(vjust = 0.5) : unused argument (vjust = 0.5) Calls: geom_text -> layer -> position_fill Execution halted

The creation of HTML files plus embedded summary plots took 0.80  wallclock secs

The creation of HTML files plus embedded summary plots finished at: Time: 23:21 hs | Date: 2021-10-19

Any hints?

Bests, Jan

lgpdevtools commented 3 years ago

Hi gaworj,

Thank you very much for your interest in using this tool. Regarding your bug, it seems to be related to some R package. Could you please tell me which version of ggplot2 have you installed via conda?

gaworj commented 3 years ago

Hi,

Thank you very much for your helpfulness. Here is the terminal output after "conda list" in my srax env:

packages in environment at /home/jang/anaconda3/envs/srax:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge argtable2 2.13 h14c3975_1001 conda-forge blast 2.10.1 pl526he19e7b1_3 bioconda boost-cpp 1.74.0 h312852a_4 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge cairo 1.16.0 h6cf1ce9_1008 conda-forge clustalo 1.2.4 h1b792b2_4 bioconda curl 7.71.1 he644dc0_3 conda-forge diamond 2.0.12 hdcc8f71_0 bioconda entrez-direct 15.6 he881be0_1 bioconda font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gettext 0.19.8.1 h73d1719_1008 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge harfbuzz 3.0.0 h83ec7ef_1 conda-forge icu 68.1 h58526e2_0 conda-forge jbig 2.1 h7f98852_2003 conda-forge jpeg 9d h36c2ea0_0 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lerc 3.0 h9c3ff4c_0 conda-forge libcurl 7.71.1 hcdd3856_3 conda-forge libdeflate 1.8 h7f98852_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libffi 3.4.2 h9c3ff4c_4 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 11.2.0 h1d223b6_11 conda-forge libglib 2.70.0 h174f98d_0 conda-forge libgomp 11.2.0 h1d223b6_11 conda-forge libiconv 1.16 h516909a_0 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libssh2 1.10.0 ha56f1ee_2 conda-forge libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge libtiff 4.3.0 h6f004c6_2 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.2.1 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge libzlib 1.2.11 h36c2ea0_1013 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge mafft 7.487 h779adbc_0 bioconda muscle 3.8.1551 h7d875b9_6 bioconda ncurses 6.2 h58526e2_4 conda-forge openssl 1.1.1l h7f98852_0 conda-forge pango 1.48.10 h54213e6_2 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-apache-test 1.40 pl526_1 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-base 2.23 pl526_1 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-class-load 0.25 pl526_0 bioconda perl-class-load-xs 0.10 pl526h6bb024c_2 bioconda perl-class-method-modifiers 2.12 pl526_0 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda perl-constant 1.33 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-data-optlist 0.110 pl526_2 bioconda perl-devel-globaldestruction 0.14 pl526_0 bioconda perl-devel-overloadinfo 0.005 pl526_0 bioconda perl-devel-stacktrace 2.04 pl526_0 bioconda perl-digest-hmac 1.03 pl526_3 bioconda perl-digest-md5 2.55 pl526_0 bioconda perl-dist-checkconflicts 0.11 pl526_2 bioconda perl-encode 2.88 pl526_1 bioconda perl-encode-locale 1.05 pl526_6 bioconda perl-env-path 0.19 pl526_2 bioconda perl-eval-closure 0.14 pl526h6bb024c_4 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-listing 6.04 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-slurp 9999.27 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-getopt-long 2.50 pl526_1 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-http-cookies 6.04 pl526_0 bioconda perl-http-daemon 6.01 pl526_1 bioconda perl-http-date 6.02 pl526_3 bioconda perl-http-message 6.18 pl526_0 bioconda perl-http-negotiate 6.01 pl526_3 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-socket-ssl 2.066 pl526_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-libwww-perl 6.39 pl526_0 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-lwp-mediatypes 6.04 pl526_0 bioconda perl-lwp-protocol-https 6.07 pl526_4 bioconda perl-lwp-simple 6.15 pl526h470a237_4 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-runtime 0.016 pl526_1 bioconda perl-module-runtime-conflicts 0.003 pl526_0 bioconda perl-moo 2.003004 pl526_0 bioconda perl-moose 2.2011 pl526hf484d3e_1 bioconda perl-mozilla-ca 20180117 pl526_1 bioconda perl-mro-compat 0.13 pl526_0 bioconda perl-net-http 6.19 pl526_0 bioconda perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda perl-ntlm 1.09 pl526_4 bioconda perl-package-deprecationmanager 0.17 pl526_0 bioconda perl-package-stash 0.38 pl526hf484d3e_1 bioconda perl-package-stash-xs 0.28 pl526hf484d3e_1 bioconda perl-parallel-forkmanager 2.02 pl526_0 bioconda perl-params-util 1.07 pl526h6bb024c_4 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-role-tiny 2.000008 pl526_0 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-socket 2.027 pl526_1 bioconda perl-storable 3.15 pl526h14c3975_0 bioconda perl-sub-exporter 0.987 pl526_2 bioconda perl-sub-exporter-progressive 0.001013 pl526_0 bioconda perl-sub-identify 0.14 pl526h14c3975_0 bioconda perl-sub-install 0.928 pl526_2 bioconda perl-sub-name 0.21 pl526_1 bioconda perl-sub-quote 2.006003 pl526_1 bioconda perl-test-harness 3.42 pl526_0 bioconda perl-test-requiresinternet 0.05 pl526_0 bioconda perl-text-csv 2.00 pl526_0 bioconda perl-time-local 1.28 pl526_1 bioconda perl-try-tiny 0.30 pl526_1 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-uri 1.76 pl526_0 bioconda perl-www-robotrules 6.02 pl526_3 bioconda perl-xsloader 0.24 pl526_0 bioconda pixman 0.40.0 h36c2ea0_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge r 3.2.2 0
r-assertthat 0.1 r3.2.2_1a
r-base 3.2.2 0
r-bh 1.60.0_2 r3.2.2_0 bioconda r-boot 1.3_17 r3.2.2_0a
r-class 7.3_14 r3.2.2_0a
r-cluster 2.0.3 r3.2.2_0a
r-codetools 0.2_14 r3.2.2_0a
r-colorspace 1.2_6 r3.2.2_0a
r-dbi 0.3.1 r3.2.2_2a
r-dichromat 2.0_0 r3.2.2_2a
r-digest 0.6.9 r3.2.2_0 bioconda r-dplyr 0.4.3 r3.2.2_0a
r-foreign 0.8_66 r3.2.2_0a
r-ggplot2 2.1.0 r3.2.2_0 bioconda r-gridextra 2.0.0 r3.2.2_0a
r-gtable 0.1.2 r3.2.2_2a
r-kernsmooth 2.23_15 r3.2.2_0a
r-labeling 0.3 r3.2.2_1a
r-lattice 0.20_33 r3.2.2_0a
r-lazyeval 0.1.10 r3.2.2_2a
r-magrittr 1.5 r3.2.2_0 bioconda r-mass 7.3_45 r3.2.2_0a
r-matrix 1.2_2 r3.2.2_0a
r-mgcv 1.8_9 r3.2.2_0a
r-munsell 0.4.2 r3.2.2_1a
r-nlme 3.1_122 r3.2.2_0a
r-nnet 7.3_11 r3.2.2_0a
r-plyr 1.8.3 r3.2.2_0a
r-r6 2.1.1 r3.2.2_0a
r-rcolorbrewer 1.1_2 r3.2.2_2a
r-rcpp 0.12.2 r3.2.2_0a
r-recommended 3.2.2 r3.2.2_0
r-reshape2 1.4.1 r3.2.2_1a
r-rpart 4.1_10 r3.2.2_0a
r-scales 0.3.0 r3.2.2_0a
r-spatial 7.3_11 r3.2.2_0a
r-stringi 1.0_1 r3.2.2_0a
r-stringr 1.0.0 r3.2.2_0a
r-survival 2.38_3 r3.2.2_0a
readline 8.1 h46c0cb4_0 conda-forge srax 1.5 0 lgpdevtools tk 8.6.11 h27826a3_1 conda-forge unzip 6.0 h7f98852_2 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge zlib 1.2.11 h36c2ea0_1013 conda-forge zstd 1.5.0 ha95c52a_0 conda-forge

Bests, Jan

lgpdevtools commented 3 years ago

Hi Jan,

It seems that your ggplot2 version (2.1.0) is quite old (Feb 2016). Please, firstly run the following commands for later running sraX:

conda create --name sraX conda activate sraX conda install srax conda install r-ggplot2=3.2.1 conda install r-dplyr conda install r-gridExtra conda install r-stringr conda install r-gplots

I've verified that the output was correctly produced, including -of course- the creation of plots.

Let me know then if some other issues arise.

gaworj commented 3 years ago

Hi,

Thank you for your very detailed installation instructions. Now it works like a charm.

gaworj commented 3 years ago

I have one additional question: What are the exact recommendations for custom database? Do I need to prepare fasta headers in specific way? I would like to use sraX for virulence genes finding basing on VFDB database. Already used VFDB formatted db for SRST2 but the sraX has problems with proper results visualization.

lgpdevtools commented 3 years ago

Indeed, the header is important for producing plots and also hyperlinks. Please, copy an example of the header that you've employed for creating your DB and I will tell you what can be improved for getting improved results.

gaworj commented 3 years ago

Thanks in advance! There are two options:

a) VFDB database format:

VFG000948(gb|NP_663908) (fbaB) fibronectin-bing protein SfbII [FBPs (VF0243)] [Streptococcus pyogenes MGAS315]

b)SRST2 compatibile header:

104fbaBfbaB_VF0243__VFG000948 VFG000948(gb|NP_663908) (fbaB) fibronectin-bing protein SfbII [FBPs (VF0243)] [Streptococcus pyogenes MGAS315]

Each header starts of course with typical ">"

lgpdevtools commented 3 years ago

The headers should be written following this format:

gene_name|accession_ID|gene_description|sequence_determination|gene_classification|organism name

For this example, your header should be formatted like this:

fbaB|NP_663908|fibronectin-bing protein SfbII|protein_homolog|vf_gene_category|Streptococcus pyogenes