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MITOS2 fails to create plots and crashes.
When installing mitos in a fresh environment using conda create -n mitos -c bioconda -c conda-forge -c defaults mitos, execution goes well and then crashes at during plot making with:
Traceback (most recent call last):
File "/home/user/miniconda3/envs/mitos/bin/runmitos.py", line 1040, in <module>
plots=args.plots, oldstst=args.oldstst)
File "/home/user/miniconda3/envs/mitos/bin/runmitos.py", line 659, in mitos
" ".join(cmd), stdout, stderr))
Exception: Rscript returned non zero
plotstst.R mitoteste//blast/stst.dat mitoteste//plots/
stdout:
stderr: Warning message:
package ‘ggplot2’ was built under R version 4.0.5
Warning message:
package ‘reshape2’ was built under R version 4.0.5
Warning message:
package ‘scales’ was built under R version 4.0.5
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] :
substituto tem comprimento zero
Calls: print ... expand_limits_discrete_trans -> expand_limits_continuous_trans -> ifelse
Além disso: Warning message:
In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL
Execução interrompidaOS: Ubuntu 20.04 LTS
installed packages: mitos_env.yml
# 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
alsa-lib 1.2.3 h516909a_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_9 conda-forge
biopython 1.76 py27h516909a_0 conda-forge
blast 2.9.0 pl526he19e7b1_7 bioconda
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cairo 1.16.0 h9f066cc_1006 conda-forge
certifi 2019.11.28 py27h8c360ce_1 conda-forge
curl 7.76.1 h979ede3_1 conda-forge
entrez-direct 16.2 he881be0_0 bioconda
expat 2.4.7 h27087fc_0 conda-forge
fontconfig 2.13.96 h8e229c2_2 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_14 conda-forge
gcc_linux-64 9.4.0 h391b98a_9 conda-forge
gettext 0.19.8.1 hf34092f_1004 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_14 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_9 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_2 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_14 conda-forge
gxx_linux-64 9.4.0 h0316aca_9 conda-forge
harfbuzz 2.7.2 ha5b49bf_1 conda-forge
hmmer 3.2.1 he1b5a44_2 bioconda
icu 67.1 he1b5a44_0 conda-forge
infernal 1.1.4 h779adbc_0 bioconda
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9e h7f98852_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.76.1 hc4aaa36_1 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_14 conda-forge
libgcc-ng 11.2.0 h1d223b6_14 conda-forge
libgfortran-ng 11.2.0 h69a702a_14 conda-forge
libgfortran5 11.2.0 h5c6108e_14 conda-forge
libglib 2.66.3 hbe7bbb4_0 conda-forge
libgomp 11.2.0 h1d223b6_14 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsanitizer 9.4.0 h79bfe98_14 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_14 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_14 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.10 h68273f3_2 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mitos 2.0.8 pyhdfd78af_1 bioconda
ncurses 6.3 h9c3ff4c_0 conda-forge
numpy 1.16.5 py27h95a1406_0 conda-forge
openjdk 11.0.8 hacce0ff_0 conda-forge
openssl 1.1.1n h166bdaf_0 conda-forge
pango 1.42.4 h69149e4_5 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.36 h032f7d1_1 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-archive-tar 2.32 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-exporter-tiny 1.002001 pl526_0 bioconda
perl-io-compress 2.087 pl526he1b5a44_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-list-moreutils 0.413 1 bioconda
perl-pathtools 3.40 0 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
python 2.7.15 h5a48372_1011_cpython conda-forge
python_abi 2.7 1_cp27mu conda-forge
r-backports 1.4.1 r40hcfec24a_0 conda-forge
r-base 4.0.3 ha43b4e8_3 conda-forge
r-brio 1.1.3 r40hcfec24a_0 conda-forge
r-callr 3.7.0 r40hc72bb7e_0 conda-forge
r-cli 3.2.0 r40h03ef668_0 conda-forge
r-colorspace 2.0_3 r40h06615bd_0 conda-forge
r-crayon 1.5.1 r40hc72bb7e_0 conda-forge
r-desc 1.4.1 r40hc72bb7e_0 conda-forge
r-diffobj 0.3.5 r40hcfec24a_0 conda-forge
r-digest 0.6.29 r40h03ef668_0 conda-forge
r-ellipsis 0.3.2 r40hcfec24a_0 conda-forge
r-evaluate 0.15 r40hc72bb7e_0 conda-forge
r-fansi 1.0.3 r40h06615bd_0 conda-forge
r-farver 2.1.0 r40h03ef668_0 conda-forge
r-ggplot2 3.3.5 r40hc72bb7e_0 conda-forge
r-glue 1.6.2 r40h06615bd_0 conda-forge
r-gtable 0.3.0 r40hc72bb7e_3 conda-forge
r-isoband 0.2.5 r40h03ef668_0 conda-forge
r-jsonlite 1.8.0 r40h06615bd_0 conda-forge
r-labeling 0.4.2 r40hc72bb7e_1 conda-forge
r-lattice 0.20_45 r40hcfec24a_0 conda-forge
r-lifecycle 1.0.1 r40hc72bb7e_0 conda-forge
r-magrittr 2.0.2 r40hcfec24a_0 conda-forge
r-mass 7.3_56 r40h06615bd_0 conda-forge
r-matrix 1.4_1 r40h0154571_0 conda-forge
r-mgcv 1.8_39 r40h0154571_0 conda-forge
r-munsell 0.5.0 r40hc72bb7e_1004 conda-forge
r-nlme 3.1_157 r40h8da6f51_0 conda-forge
r-pillar 1.7.0 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge
r-pkgload 1.2.4 r40h03ef668_0 conda-forge
r-plyr 1.8.7 r40h7525677_0 conda-forge
r-praise 1.0.0 r40hc72bb7e_1005 conda-forge
r-processx 3.5.3 r40h06615bd_0 conda-forge
r-ps 1.6.0 r40hcfec24a_0 conda-forge
r-r6 2.5.1 r40hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r40h785f33e_1003 conda-forge
r-rcpp 1.0.8.3 r40h7525677_0 conda-forge
r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge
r-reshape2 1.4.4 r40h03ef668_1 conda-forge
r-rlang 1.0.2 r40h7525677_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40hc72bb7e_0 conda-forge
r-stringi 1.5.3 r40hca8494e_0 conda-forge
r-stringr 1.4.0 r40hc72bb7e_2 conda-forge
r-testthat 3.1.2 r40h03ef668_0 conda-forge
r-tibble 3.1.6 r40hcfec24a_0 conda-forge
r-utf8 1.2.2 r40hcfec24a_0 conda-forge
r-vctrs 0.3.8 r40hcfec24a_1 conda-forge
r-viridislite 0.4.0 r40hc72bb7e_0 conda-forge
r-waldo 0.4.0 r40hc72bb7e_0 conda-forge
r-withr 2.5.0 r40hc72bb7e_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 44.0.0 py27_0 conda-forge
sqlite 3.37.1 h4ff8645_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
viennarna 1.8.5 h470a237_1 bioconda
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 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-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 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 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge