failed to install Anvio 6.2 and failed to install Anvio master
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c.hof...@usp.br
Aug 20, 2020, 2:00:01 PM8/20/20
to Anvi'o
Dear Meren and Forum,
I have been trying for the past week to get Anvio to install on a cluster I have access to (no su, though) and have not been able to successfully run the mini test.
For the basic 6.2 instalation i get:
(anvio62) christian.hoffmann@scm00:~> anvi-self-test -v
Anvi'o version ...............................: esther (v6.2)
Profile DB version ...........................: 31
Contigs DB version ...........................: 14
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1
(anvio62) christian.hoffmann@scm00:~> anvi-self-test --suite mini
Segmentation fault
(anvio62) christian.hoffmann@scm00:~> anvi-self-test --suite mini
Inconsistency detected by ld.so: dl-open.c: 583: _dl_open: Assertion `_dl_debug_initialize (0, args.nsid)->r_state == RT_CONSISTENT' failed!
The only note worthy issue that comes up is "The environment is inconsistent" warning when running this:
conda install -y -c bioconda -c conda-forge anvio-minimal==6.2=py_1
Collecting package metadata (current_repodata.json): done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- bioconda/noarch::anvio==6.2=0
For the Anvio master installation I get this error:
anvi-self-test --suite mini --debug
Inconsistency detected by ld.so: dl-open.c: 583: _dl_open: Assertion `_dl_debug_initialize (0, args.nsid)->r_state == RT_CONSISTENT' failed!
However, anvi-self-test -v
works as well:
(anvio) christian.hoffmann@scm01:~/github/anvio/bin> anvi-self-test -v
Anvi'o version ...............................: esther (v6.2-master)
Profile DB version ...........................: 34
Contigs DB version ...........................: 18
Pan DB version ...............................: 14
Genome data storage version ..................: 7
Auxiliary data storage version ...............: 2
Structure DB version .........................: 2
Kegg Modules DB version ......................: 2
Many thanks for the help!
Best,
Chris
from the system where I'm trying to get to work:
(anvio62) christian.hoffmann@scm00:~> cat /etc/*-release
LSB_VERSION="core-2.0-noarch:core-3.2-noarch:core-4.0-noarch:core-2.0-x86_64:core-3.2-x86_64:core-4.0-x86_64"
SUSE Linux Enterprise Server 11 (x86_64)
VERSION = 11
PATCHLEVEL = 2
And this is the
> conda list
output for the Anvio master installation, in case it helps.
(anvio) christian.hoffmann@scm01:~/github/anvio/bin> conda list
# packages in environment at /home/iaf/christian.hoffmann/miniconda3/envs/anvio:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_r-mutex 1.0.0 anacondar_1
aioeasywebdav 2.4.0 py36_1000 conda-forge
aiohttp 3.6.2 py36h7b6447c_0
appdirs 1.4.4 py_0
asgiref 3.2.10 py_0
async-timeout 3.0.1 py36_0
attrs 19.3.0 py_0
bcrypt 3.1.7 py36h7b6447c_1
binutils_impl_linux-64 2.33.1 he6710b0_7
binutils_linux-64 2.33.1 h9595d00_15
bioconductor-qvalue 2.18.0 r36_1 bioconda
biopython 1.77 py36h7b6447c_0
blas 2.11 openblas conda-forge
blast 2.9.0 pl526h3066fca_4 bioconda
blast-legacy 2.2.26 2 bioconda
boost 1.70.0 py36h9de70de_1 conda-forge
boost-cpp 1.70.0 ha2d47e9_1 conda-forge
boto3 1.14.43 py_0
botocore 1.17.45 py_0
bottle 0.12.18 py_0 conda-forge
bowtie2 2.4.1 py36h5202f60_3 bioconda
brotlipy 0.7.0 py36h7b6447c_1000
bwa 0.7.17 hed695b0_7 bioconda
bwidget 1.9.11 1
bzip2 1.0.8 h7b6447c_0
ca-certificates 2020.6.24 0
cachetools 4.1.1 py_0
cairo 1.16.0 h18b612c_1001 conda-forge
centrifuge 1.0.4_beta py36pl526he941832_2 bioconda
certifi 2020.6.20 py36_0
cffi 1.14.0 py36h2e261b9_0
chardet 3.0.4 py36_1003
colored 1.4.2 py_0 conda-forge
configargparse 1.2.3 py_0
cryptography 2.9.2 py36h1ba5d50_0
curl 7.67.0 hbc83047_0
cycler 0.10.0 py36_0
datrie 0.8.2 py36h7b6447c_0
dbus 1.13.16 hb2f20db_0
decorator 4.4.2 py_0
diamond 0.9.14 h8b12597_3 bioconda
django 3.0.3 py_0
docutils 0.15.2 py36_0
dropbox 10.2.0 py36_0
entrez-direct 13.3 pl526h375a9b1_0 bioconda
ete3 3.1.1 py36_0 bioconda
expat 2.2.9 he6710b0_2
fastani 1.31 he1c1bb9_0 bioconda
fasttree 2.1.10 h516909a_4 bioconda
fftw 3.3.8 h7b6447c_3
filechunkio 1.6 py36_0 bioconda
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.10.2 h5ab3b9f_0
ftputil 3.2 py36_0 bioconda
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_15
gettext 0.19.8.1 hd7bead4_3
gfortran_impl_linux-64 7.3.0 hdf63c60_1
gfortran_linux-64 7.3.0 h553295d_15
ghostscript 9.18 1 bioconda
giflib 5.1.4 h14c3975_1
gitdb 4.0.5 py_0
gitpython 3.1.3 py_1
glib 2.63.1 h5a9c865_0
google-api-core 1.17.0 py36_0
google-auth 1.20.1 py_0
google-cloud-core 1.3.0 py_0
google-cloud-storage 1.28.1 py_0
google-resumable-media 0.5.1 py_0
googleapis-common-protos 1.51.0 py36_2
graphite2 1.3.14 h23475e2_0
graphviz 2.40.1 h0dab3d1_0 conda-forge
gsl 2.5 h294904e_1 conda-forge
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_15
harfbuzz 1.8.8 hffaf4a1_0
hmmer 3.3 he1b5a44_1 bioconda
htslib 1.10.2 h78d89cc_0 bioconda
icu 58.2 he6710b0_3
idna 2.10 py_0
idna_ssl 1.1.0 py36_0
illumina-utils 2.7 py_0 bioconda
imagemagick 7.0.8_11 pl526hc610aec_0 conda-forge
importlib-metadata 1.7.0 py36_0
importlib_metadata 1.7.0 0
infernal 1.1.2 h516909a_3 bioconda
intel-openmp 2020.1 217
ipython_genutils 0.2.0 py36_0
iqtree 2.0.3 h176a8bc_0 bioconda
jbig 2.1 hdba287a_0
jinja2 2.11.2 py_0
jmespath 0.10.0 py_0
joblib 0.16.0 py_0
jpeg 9d h516909a_0 conda-forge
jsonschema 3.2.0 py36_0
jupyter_core 4.6.3 py36_0
kiwisolver 1.2.0 py36hfd86e86_0
krb5 1.16.4 h173b8e3_0
ld_impl_linux-64 2.33.1 h53a641e_7
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libcurl 7.67.0 h20c2e04_0
libdeflate 1.3 h516909a_0 conda-forge
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
liblapack 3.8.0 11_openblas conda-forge
liblapacke 3.8.0 11_openblas conda-forge
libllvm9 9.0.1 h4a3c616_1
libopenblas 0.3.6 h5a2b251_2
libpng 1.6.37 hbc83047_0
libprotobuf 3.12.4 hd408876_0
libsodium 1.0.18 h7b6447c_0
libssh2 1.9.0 h1ba5d50_1
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_1
libtool 2.4.6 h7b6447c_5
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp 0.5.2 7 conda-forge
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 he19cac6_1
libxslt 1.1.34 hc22bd24_0
llvmlite 0.33.0 py36hc6ec683_1
lxml 4.5.2 py36hefd8a0e_0
lz4-c 1.9.2 he6710b0_1
make 4.2.1 h1bed415_1
markupsafe 1.1.1 py36h7b6447c_0
matplotlib 3.2.2 0
matplotlib-base 3.2.2 py36hef1b27d_0
mcl 14.137 pl526h516909a_5 bioconda
megahit 1.2.9 h8b12597_0 bioconda
mistune 0.8.4 py36h7b6447c_0
mkl 2020.1 217
mkl-service 2.3.0 py36he904b0f_0
mkl_fft 1.0.10 py36_0 conda-forge
mkl_random 1.1.1 py36h830a2c2_0 conda-forge
multidict 4.7.3 py36h7b6447c_0
mummer 3.23 pl526he1b5a44_11 bioconda
muscle 3.8.1551 hc9558a2_5 bioconda
nbformat 5.0.7 py_0
ncurses 6.1 he6710b0_1
networkx 2.4 py_1
numba 0.50.1 py36h0573a6f_1
numpy 1.19.1 py36h30dfecb_0
numpy-base 1.19.1 py36h75fe3a5_0
openjpeg 2.3.0 h05c96fa_1
openssl 1.1.1g h7b6447c_0
pandas 0.25.1 py36he6710b0_0
pango 1.40.14 he752989_2 conda-forge
paramiko 2.7.1 py_0
paste 3.2.2 py36_0
patsy 0.5.1 py36_0
pcre 8.44 he6710b0_0
perl 5.26.2 h14c3975_0
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-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-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 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-temp 0.2304 pl526_2 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 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-mime-base64 3.15 pl526_1 bioconda
perl-mozilla-ca 20180117 pl526_1 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-parent 0.236 pl526_1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 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-test-requiresinternet 0.05 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-xml-namespacesupport 1.12 pl526_0 bioconda
perl-xml-parser 2.44 pl526h4e0c4b3_7 bioconda
perl-xml-sax 1.02 pl526_0 bioconda
perl-xml-sax-base 1.09 pl526_0 bioconda
perl-xml-sax-expat 0.51 pl526_3 bioconda
perl-xml-simple 2.25 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
pip 20.2.2 py36_0
pixman 0.38.0 h7b6447c_0
pkg-config 0.29.2 h1bed415_8
prettytable 0.7.2 py_3 conda-forge
prodigal 2.6.3 h516909a_2 bioconda
protobuf 3.12.4 py36he6710b0_0
psutil 5.4.3 py36h14c3975_0
pyani 0.2.10 py_0 bioconda
pyasn1 0.4.8 py_0
pyasn1-modules 0.2.7 py_0
pycparser 2.20 py_2
pygments 2.6.1 py_0
pygraphviz 1.3 py36h14c3975_1
pynacl 1.4.0 py36h7b6447c_1
pyopenssl 19.1.0 py_1
pyparsing 2.4.7 py_0
pyqt 5.9.2 py36h05f1152_2
pyrsistent 0.16.0 py36h7b6447c_0
pysam 0.15.3 py36hbcae180_3 bioconda
pysftp 0.2.9 py_1
pysocks 1.7.1 py36_0
python 3.6.7 h357f687_1008_cpython conda-forge
python-dateutil 2.8.1 py_0
python-irodsclient 0.8.2 py_0 conda-forge
python-levenshtein 0.12.0 py36h7b6447c_1001
python_abi 3.6 1_cp36m conda-forge
pytz 2020.1 py_0
pyyaml 5.3.1 py36h7b6447c_1
qt 5.9.7 h5867ecd_1
r-askpass 1.0 r36h14c3975_0
r-assertthat 0.2.1 r36h6115d3f_0
r-backports 1.1.4 r36h96ca727_0
r-base 3.6.1 h8900bf8_2 conda-forge
r-base64enc 0.1_3 r36h96ca727_4
r-bh 1.69.0_1 r36h6115d3f_0
r-broom 0.5.2 r36h6115d3f_0
r-callr 3.2.0 r36h6115d3f_0
r-cellranger 1.1.0 r36h6115d3f_0
r-cli 1.1.0 r36h6115d3f_0
r-clipr 0.6.0 r36h6115d3f_0
r-colorspace 1.4_1 r36h96ca727_0
r-crayon 1.3.4 r36h6115d3f_0
r-curl 3.3 r36h96ca727_0
r-dbi 1.0.0 r36h6115d3f_0
r-dbplyr 1.4.0 r36h6115d3f_0
r-dichromat 2.0_0 r36h6115d3f_4
r-digest 0.6.18 r36h96ca727_0
r-dplyr 0.8.0.1 r36h29659fb_0
r-ellipsis 0.1.0 r36h96ca727_0
r-evaluate 0.13 r36h6115d3f_0
r-fansi 0.4.0 r36h96ca727_0
r-forcats 0.4.0 r36h6115d3f_0
r-fs 1.2.7 r36h29659fb_0
r-generics 0.0.2 r36h6115d3f_0
r-getopt 1.20.3 r36h6115d3f_0
r-ggplot2 3.1.1 r36h6115d3f_0
r-glue 1.3.1 r36h96ca727_0
r-gtable 0.3.0 r36h6115d3f_0
r-haven 2.1.0 r36h29659fb_0
r-highr 0.8 r36h6115d3f_0
r-hms 0.4.2 r36h6115d3f_0
r-htmltools 0.3.6 r36h29659fb_0
r-httr 1.4.0 r36h6115d3f_0
r-jsonlite 1.6 r36h96ca727_0
r-knitr 1.22 r36h6115d3f_0
r-labeling 0.3 r36h6115d3f_4
r-lattice 0.20_38 r36h96ca727_0
r-lazyeval 0.2.2 r36h96ca727_0
r-lubridate 1.7.4 r36h29659fb_0
r-magrittr 1.5 r36h6115d3f_4
r-markdown 0.9 r36h96ca727_0
r-mass 7.3_51.3 r36h96ca727_0
r-matrix 1.2_17 r36h96ca727_0
r-mgcv 1.8_28 r36h96ca727_0
r-mime 0.6 r36h96ca727_0
r-modelr 0.1.4 r36h6115d3f_0
r-munsell 0.5.0 r36h6115d3f_0
r-nlme 3.1_139 r36ha65eedd_0
r-openssl 1.3 r36h96ca727_0
r-optparse 1.6.2 r36h6115d3f_0
r-pillar 1.3.1 r36h6115d3f_0
r-pkgconfig 2.0.2 r36h6115d3f_0
r-plogr 0.2.0 r36h6115d3f_0
r-plyr 1.8.4 r36h29659fb_0
r-prettyunits 1.0.2 r36h6115d3f_0
r-processx 3.3.0 r36h96ca727_0
r-progress 1.2.0 r36h6115d3f_0
r-ps 1.3.0 r36h96ca727_0
r-purrr 0.3.2 r36h96ca727_0
r-r6 2.4.0 r36h6115d3f_0
r-rcolorbrewer 1.1_2 r36h6115d3f_0
r-rcpp 1.0.1 r36h29659fb_0
r-readr 1.3.1 r36h29659fb_0
r-readxl 1.3.1 r36h29659fb_0
r-rematch 1.0.1 r36h6115d3f_0
r-reprex 0.2.1 r36h6115d3f_0
r-reshape2 1.4.3 r36h29659fb_0
r-rlang 0.3.4 r36h96ca727_0
r-rmarkdown 1.12 r36h6115d3f_0
r-rstudioapi 0.10 r36h6115d3f_0
r-rvest 0.3.3 r36h6115d3f_0
r-scales 1.0.0 r36h29659fb_0
r-selectr 0.4_1 r36h6115d3f_0
r-stringi 1.4.3 r36h29659fb_0
r-stringr 1.4.0 r36h6115d3f_0
r-sys 3.2 r36h96ca727_0
r-tibble 2.1.1 r36h96ca727_0
r-tidyr 0.8.3 r36h29659fb_0
r-tidyselect 0.2.5 r36h29659fb_0
r-tidyverse 1.2.1 r36h6115d3f_0
r-tinytex 0.12 r36h6115d3f_0
r-utf8 1.1.4 r36h96ca727_0
r-viridislite 0.3.0 r36h6115d3f_0
r-whisker 0.3_2 r36h6115d3f_4
r-withr 2.1.2 r36h6115d3f_0
r-xfun 0.6 r36h6115d3f_0
r-xml2 1.2.0 r36h29659fb_0
r-yaml 2.2.0 r36h96ca727_0
ratelimiter 1.2.0 py36h9f0ad1d_1001 conda-forge
readline 8.0 h7b6447c_0
requests 2.24.0 py_0
rsa 4.6 py_0
s3transfer 0.3.3 py36_0
samtools 1.10 h9402c20_2 bioconda
scikit-learn 0.23.1 py36h7ea95a0_0
scipy 1.5.0 py36habc2bb6_0
seaborn 0.10.1 py_0
sed 4.4 h7b6447c_2
setuptools 49.6.0 py36_0
sip 4.19.8 py36hf484d3e_0
six 1.15.0 py_0
smmap 3.0.4 py_0
snakemake 5.10.0 0 bioconda
snakemake-minimal 5.10.0 py_0 bioconda
sqlite 3.31.1 h7b6447c_0
sqlparse 0.3.1 py_0
statsmodels 0.11.1 py36h7b6447c_0
tabulate 0.8.7 py36_0
tbb 2020.1 hc9558a2_0 conda-forge
threadpoolctl 2.1.0 pyh5ca1d4c_0
tk 8.6.10 hbc83047_0
tktable 2.10 h14c3975_0
toposort 1.5 py_3 conda-forge
tornado 6.0.4 py36h7b6447c_1
traitlets 4.3.3 py36_0
trimal 1.4.1 hc9558a2_4 bioconda
trnascan-se 2.0.5 pl526h516909a_0 bioconda
typing_extensions 3.7.4.2 py_0
urllib3 1.25.10 py_0
wheel 0.34.2 py36_0
wrapt 1.12.1 py36h7b6447c_1
xmlrunner 1.7.7 py_0 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.11 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxpm 3.5.13 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-libxt 1.1.5 h516909a_1003 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
yarl 1.4.2 py36h7b6447c_0
zipp 3.1.0 py_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.5 h9ceee32_0
c.hof...@usp.br
Aug 24, 2020, 12:08:40 PM8/24/20
to Anvi'o
Dear group,
After many, maaany, Maaaaany installation tries, in a variety of ways, I finally got Anvi'o to work (I think).
I'll post what worked for me here as a reference to others.
It is basically the anvio-master installation with a tweak on the dependencies installation.
No idea why it happened as such, or even what exactly happened. I still need to set up a tunnel to properly display the interactive interface, so it is possible that I am just getting giberish, but I don't think so (I'll follow up here if anything else comes up).
best,
Chris
### what I did ###
### commands, clipped outputs, plus some comments ###
> conda create -y --name anvio-master python=3.6
> conda activate anvio-master
(anvio-master) :~> conda install -y prodigal \
mcl \
muscle \
hmmer \
diamond==0.9.14 \
blast \
megahit \
bowtie2 \
bwa \
samtools \
centrifuge \
trimal \
iqtree \
fastani \
fasttree \
r-base \
r-stringi \
r-tidyverse \
r-magrittr \
r-optparse \
bioconductor-qvalue \
trnascan-se
(anvio-master) :~> pip install -r github/anvio/requirements.txt
### this doesn't work for me, and gives a pretty extensive an error, which I clipped the last part here:
...
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config': 'llvm-config'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/iaf/christian.hoffmann/tmp/pip-install-1xzfm345/llvmlite/ffi/build.py", line 191, in <module>
main()
File "/home/iaf/christian.hoffmann/tmp/pip-install-1xzfm345/llvmlite/ffi/build.py", line 181, in main
main_posix('linux', '.so')
File "/home/iaf/christian.hoffmann/tmp/pip-install-1xzfm345/llvmlite/ffi/build.py", line 108, in main_posix
"to the path for llvm-config" % (llvm_config,))
RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
error: command '/home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/bin/python' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/iaf/christian.hoffmann/tmp/pip-install-1xzfm345/llvmlite/setup.py'"'"'; __file__='"'"'/home/iaf/christian.hoffmann/tmp/pip-install-1xzfm345/llvmlite/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /home/iaf/christian.hoffmann/tmp/pip-record-ojbcqkv9/install-record.txt --single-version-externally-managed --compile --install-headers /home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/include/python3.6m/llvmlite Check the logs for full command output.
### I used this command to install llvmlite:
(anvio-master) :~> conda install --channel=numba llvmlite
### and repeated the last step:
(anvio-master) :~> pip install -r github/anvio/requirements.txt
cat <<EOF >${CONDA_PREFIX}/etc/conda/activate.d/anvio.sh
# creating an activation script for the the anvi'o master conda environmnet
# so (1) Python knows where to find anvi'o libraries, (2) BASH knows
# where to find its programs, and (3) every time the environment is activated
# it downloads the latest code from the master repository
export PYTHONPATH=\$PYTHONPATH:~/github/anvio/
export PATH=\$PATH:~/github/anvio/bin:~/github/anvio/sandbox
echo -e "\033[1;34mUpdating from the master repository in GitHub \033[0;31m(press CTRL+C to cancel)\033[0m ..."
cd ~/github/anvio && git pull && cd -
EOF
### created the bash shortcut etc
(anvio-master) :~> source ~/.bash_profile
(anvio-master) :~> anvi-activate-master
(anvio-master) :~> anvi-self-test -v
Anvi'o version ...............................: esther (v6.2-master)
Profile DB version ...........................: 34
Contigs DB version ...........................: 18
Pan DB version ...............................: 14
Genome data storage version ..................: 7
Auxiliary data storage version ...............: 2
Structure DB version .........................: 2
Kegg Modules DB version ......................: 2
(anvio-master) :~> anvi-self-test --suite mini
### And finally, I got a bunch of output here as expected.
### But it chocked on a "segmentation fault" towards the end:
...
* 3 entries added into layers additional data as data group 't_species'
WARNING
===============================================
A total of 2 taxon names, which made up 0.12% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.
./run_mini_test.sh: line 33: 29356 Segmentation fault anvi-import-taxonomy-for-layers -p $output_dir/SAMPLE-$f/PROFILE.db -i $files/example_files_for_kraken_hll_taxonomy/SAMPLE-$f.mpa --parser krakenuniq
Config Error: According to the exit code ('139'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.
### So, I tested running the mini test SH script directly (saw a suggestion from @Meren to someone to do this - maybe it was on github? - to see if things were running properly...).
cd ~/github/anvio/anvio/tests
(anvio-master) :~/github/anvio/anvio/tests> ./run_mini_test.sh
...
Collection: "CONCOCT"
===============================================
Collection ID ................................: CONCOCT
Number of bins ...............................: 3
Number of splits described ...................: 35
Bin names ....................................: Bin_1, Bin_2, Bin_3
:: Firing up the interactive interface ...
./run_mini_test.sh: line 79: 32153 Segmentation fault anvi-interactive -p $output_dir/SAMPLES-MERGED/PROFILE.db -c $output_dir/CONTIGS.db
### Segmentation fault error again, but it seemed this was just anvio interactive:
### So finally: I just called anvi-interactive with the files that were created above:
(anvio-master) :~/github/anvio/anvio/tests> anvi-interactive -p tests/sandbox/test-output/SAMPLES-MERGED/PROFILE.db -c tests/sandbox/test-output/CONTIGS.db
...
Contigs DB ...................................: Initialized:
...
* The server is up and running 🎉
...
Server address ...............................: http://0.0.0.0:8080
A. Murat Eren
Aug 24, 2020, 4:02:57 PM8/24/20
to Anvi'o
Dear Dr. Hoffmann,
Thank you very much for your summary, congratulations for solving it, and apologies for not being very helpful with this earlier :)
I hope others who may run into this issue will be able to follow your recipe.
Best wishes,
--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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c.hof...@usp.br
Aug 25, 2020, 12:45:19 PM8/25/20
to Anvi'o
Dear Meren,
I spoke too soon, it seems.
I keep getting segmentation fault errors and I'm really running out of ideas here (I can't even remotely pretend to be a python wizard here)...
On to the problems:
I picked up where i left yesterday, to set up a tunnel to proceed to Anvi'o interactive.
Well, when I logged in again, Anvi'o master updated:
christian.hoffmann@scm00:~> anvi-activate-master
Updating from the master repository in GitHub (press CTRL+C to cancel) ...
remote: Enumerating objects: 28, done.
remote: Counting objects: 100% (28/28), done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 28 (delta 17), reused 28 (delta 17), pack-reused 0
Unpacking objects: 100% (28/28), done.
0729df4ef..4a1d29d87 master -> origin/master
99212f985..d9cf6cc0f structure -> origin/structure
Updating 0729df4ef..4a1d29d87
Fast-forward
AUTHORS.txt | 53 +++++++++++-----------
.../programs/anvi-get-sequences-for-hmm-hits.md | 2 +
2 files changed, 29 insertions(+), 26 deletions(-)
and nothing really worked well after that.
after much fiddling around (including with samtools), I ran each command inside the "run_mini_test.sh" script and I cannot get passed this command:
(anvio-master) christian.hoffmann@scm00:~/github/anvio/anvio/tests> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -H sandbox/external_hmm_profile --just-do-it
Segmentation fault
Bellow it the detailed steps I took in case they help.
I'm just not versed enough to even know where to begin to look for the cause of this segmentation fault.
Any help is much appreciated.
Thanks!
Chris
(anvio-master) christian.hoffmann@scm01:~> anvi-interactive -p /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPLES-MERGED/PROFILE.db -c /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/CONTIGS.db
Segmentation fault
#### run mini test again
(anvio-master) christian.hoffmann@scm01:~> anvi-self-test --suite mini
:: Output directory ...
/home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output
:: Anvo'o version ...
Anvi'o version ...............................: esther (v6.2-master)
Profile DB version ...........................: 34
Contigs DB version ...........................: 18
Pan DB version ...............................: 14
Genome data storage version ..................: 7
Auxiliary data storage version ...............: 2
Structure DB version .........................: 2
Kegg Modules DB version ......................: 2
:: Initializing raw BAM files ...
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/SAMPLE-01.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/SAMPLE-01.bam.bai
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/SAMPLE-02.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/SAMPLE-02.bam.bai
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/SAMPLE-03.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/SAMPLE-03.bam.bai
:: Generating an EMPTY contigs database ...
Input FASTA file .............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB for anvi'o mini self-test
Description ..................................: No description is given
Num threads for gene calling .................: 1
Finding ORFs in contigs
===============================================
Genes ........................................: /home/iaf/christian.hoffmann/tmp/tmpf57wzgat/contigs.genes
Amino acid sequences .........................: /home/iaf/christian.hoffmann/tmp/tmpf57wzgat/contigs.amino_acid_sequences
Log file .....................................: /home/iaf/christian.hoffmann/tmp/tmpf57wzgat/00_log.txt
CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.
Result .......................................: Prodigal (v2.6.3) has identified 51 genes.
CONTIGS DB CREATE REPORT
===============================================
Split Length .................................: 1,000
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: False
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True
Contigs with at least one gene call ..........: 6 of 6 (100.0%)
Contigs database .............................: A new database,
/home/iaf/christian.hoffmann/tmp/tmpp1xa4ygt/test-output/CONTIGS.db, has been
created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (what anvi'o gave back) .: 1,620
./run_mini_test.sh: line 17: 9456 Segmentation fault anvi-gen-contigs-database -f $files/contigs.fa -o $output_dir/CONTIG S.db -L 1000 --project-name "Contigs DB for anvi'o mini self-test"
Config Error: According to the exit code ('139'), anvi'o suspects that something may have gone
wrong while running your tests :/ We hope that the reason is clear to you from
the lines above. But if you don't see anything obvious, and especially if the
test ended up running until the end with reasonable looking final results, you
shouldn't worry too much about this error. Life is short and we all can worry
just a bit less.
### call script directly ~/github/anvio/anvio/tests/run_mini_test.sh
(anvio-master) christian.hoffmann@scm01:~/github/anvio/anvio/tests> ./run_mini_test.sh
:: Output directory ...
/home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output
:: Anvo'o version ...
Anvi'o version ...............................: esther (v6.2-master)
Profile DB version ...........................: 34
Contigs DB version ...........................: 18
Pan DB version ...............................: 14
Genome data storage version ..................: 7
Auxiliary data storage version ...............: 2
Structure DB version .........................: 2
Kegg Modules DB version ......................: 2
:: Initializing raw BAM files ...
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPL E-01.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPL E-01.bam.bai
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPL E-02.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPL E-02.bam.bai
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPL E-03.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/SAMPL E-03.bam.bai
:: Generating an EMPTY contigs database ...
Input FASTA file .............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB for anvi'o mini self-test
Description ..................................: No description is given
Num threads for gene calling .................: 1
Finding ORFs in contigs
===============================================
Genes ........................................: /home/iaf/christian.hoffmann/tmp/tmpoh1_z0_w/contigs.genes
Amino acid sequences .........................: /home/iaf/christian.hoffmann/tmp/tmpoh1_z0_w/contigs.amino_acid_sequences
Log file .....................................: /home/iaf/christian.hoffmann/tmp/tmpoh1_z0_w/00_log.txt
CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.
Result .......................................: Prodigal (v2.6.3) has identified 51 genes.
CONTIGS DB CREATE REPORT
===============================================
Split Length .................................: 1,000
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: False
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True
Contigs with at least one gene call ..........: 6 of 6 (100.0%)
Contigs database .............................: A new database,
/home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/test-output/CONTI GS.db,
has been created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (what anvi'o gave back) .: 1,620
:: Populating search tables in the latest contigs database using default HMM profiles ...
./run_mini_test.sh: line 20: 10027 Segmentation fault anvi-run-hmms -c $output_dir/CONTIGS.db --num-threads 2 --just-do-it
### this was not a consistent issue: sometimes it would crash when generating the contig database.
### some advice about error on generate contig database and samtools...
### checked samtool and it wasn't working properly (no idea why)
(anvio-master) christian.hoffmann@scm00:~> samtools -v
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
### some info on internet about this specific error
### trying solution proposed
(anvio-master) christian.hoffmann@scm00:~> conda config --add channels defaults
(anvio-master) christian.hoffmann@scm00:~> conda config --add channels bioconda
(anvio-master) christian.hoffmann@scm00:~> conda config --add channels conda-forge
(anvio-master) christian.hoffmann@scm00:~> conda install -c bioconda -y samtools
(anvio-master) christian.hoffmann@scm00:~> conda install openssl=1.0
### a bunch of things changed here, but no inconsistency detected
(anvio-master) christian.hoffmann@scm00:~> samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.7 (using htslib 1.7)
### checking other dependencies, just in case:
(anvio-master) christian.hoffmann@scm00:~> prodigal -v
Prodigal V2.6.3: February, 2016
(anvio-master) christian.hoffmann@scm00:~> mcl --version
mcl 14-137
Copyright (c) 1999-2014, Stijn van Dongen. mcl comes with NO WARRANTY
(anvio-master) christian.hoffmann@scm00:~> hmmsearch -h
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3 (Nov 2019); http://hmmer.org/
# Copyright (C) 2019 Howard Hughes Medical Institute.
(anvio-master) christian.hoffmann@scm00:~> diamond --version
diamond version 0.9.14
(anvio-master) christian.hoffmann@scm00:~> blastn -version
blastn: 2.5.0+
(anvio-master) christian.hoffmann@scm00:~> megahit -v
MEGAHIT v1.2.9
(anvio-master) christian.hoffmann@scm00:~> bowtie2 --version
/home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/bin/bowtie2-align-s version
64-bit
Built on
Sun Jul 26 00:11:42 UTC 2020
Compiler: gcc version 7.5.0 (crosstool-NG 1.24.0.127_c5b0242_dirty)
Options: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1595722055834/work=/usr/local/src/conda/bowtie2-2.4.1 -fdebug-prefix-map=/home/iaf/christian.hoffmann/miniconda3/envs/anvio-master=/usr/local/src/conda-prefix -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
(anvio-master) christian.hoffmann@scm00:~> bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <l...@sanger.ac.uk>
(anvio-master) christian.hoffmann@scm00:~> samtools --version
samtools 1.7
Using htslib 1.7
Copyright (C) 2018 Genome Research Ltd.
(anvio-master) christian.hoffmann@scm00:~> centrifuge --version
/home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/bin/centrifuge-class version 1.0.4
64-bit
Built on default-03141e47-51ec-4b49-bdf0-46eb46c89ddb
Wed Jul 4 15:01:13 UTC 2018
Compiler: gcc version 4.8.2 20140120 (Red Hat 4.8.2-15) (GCC)
Options: -O3 -m64 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
(anvio-master) christian.hoffmann@scm00:~> trimal --version
trimAl v1.4.rev15 build[2013-12-17]
(anvio-master) christian.hoffmann@scm00:~> iqtree --version
IQ-TREE multicore version 2.0.3 for Linux 64-bit built Apr 26 2020
(anvio-master) christian.hoffmann@scm00:~> fastANI --version
version 1.31
(anvio-master) christian.hoffmann@scm00:~> R --version
R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
### re-run mini test:
(anvio-master) christian.hoffmann@scm00:~/github/anvio/anvio/tests> ./run_mini_test.sh /home/iaf/christian.hoffmann/anvioTestOutput
:: Output directory ...
/home/iaf/christian.hoffmann/anvioTestOutput/test-output
:: Anvo'o version ...
Anvi'o version ...............................: esther (v6.2-master)
Profile DB version ...........................: 34
Contigs DB version ...........................: 18
Pan DB version ...............................: 14
Genome data storage version ..................: 7
Auxiliary data storage version ...............: 2
Structure DB version .........................: 2
Kegg Modules DB version ......................: 2
:: Initializing raw BAM files ...
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-01.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-01.bam.bai
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-02.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-02.bam.bai
Sorted BAM File ..............................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03.bam
BAM File Index ...............................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03.bam.bai
:: Generating an EMPTY contigs database ...
Input FASTA file .............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB for anvi'o mini self-test
Description ..................................: No description is given
Num threads for gene calling .................: 1
Finding ORFs in contigs
===============================================
Genes ........................................: /home/iaf/christian.hoffmann/tmp/tmpzu03wf6l/contigs.genes
Amino acid sequences .........................: /home/iaf/christian.hoffmann/tmp/tmpzu03wf6l/contigs.amino_acid_sequences
Log file .....................................: /home/iaf/christian.hoffmann/tmp/tmpzu03wf6l/00_log.txt
CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.
Result .......................................: Prodigal (v2.6.3) has identified 51 genes.
CONTIGS DB CREATE REPORT
===============================================
Split Length .................................: 1,000
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: False
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True
Contigs with at least one gene call ..........: 6 of 6 (100.0%)
Contigs database .............................: A new database, /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db, has been created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (what anvi'o gave back) .: 1,620
:: Populating search tables in the latest contigs database using default HMM profiles ...
./run_mini_test.sh: line 20: 31409 Segmentation fault anvi-run-hmms -c $output_dir/CONTIGS.db --num-threads 2 --just-do-it
#### run each command from "run_mini_test.sh"
(anvio-master) christian.hoffmann@scm00:~/github/anvio/anvio/tests> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db --num-threads 2 --just-do-it
Target found .................................: RNA:CONTIG
Target found .................................: AA:GENE
HMM Profiling for Ribosomal_RNAs
===============================================
Reference ....................................: Seemann T, https://github.com/tseemann/barrnap
Kind .........................................: Ribosomal_RNAs
Alphabet .....................................: RNA
Context ......................................: CONTIG
Domain .......................................: N/A
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmp44m_axxt/Ribosomal_RNAs.hmm
Number of genes in HMM model .................: 12
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 2
HMMer program used for search ................: nhmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmpcrgomb55
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmpcrgomb55/RNA_contig_sequences.fa.0_log
Log file for thread 1 ........................: /home/iaf/christian.hoffmann/tmp/tmpcrgomb55/RNA_contig_sequences.fa.1_log
Number of raw hits ...........................: 0
* The HMM source 'Ribosomal_RNAs' returned 0 hits. SAD (but it's stil OK).
HMM Profiling for Protista_83
===============================================
Reference ....................................: Delmont, http://merenlab.org/delmont-euk-scgs
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: eukarya
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmp44m_axxt/Protista_83.hmm
Number of genes in HMM model .................: 83
Noise cutoff term(s) .........................: -E 1e-25
Number of CPUs will be used for search .......: 2
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5/AA_gene_sequences.fa.0_log
Log file for thread 1 ........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5/AA_gene_sequences.fa.1_log
Number of raw hits ...........................: 0
* The HMM source 'Protista_83' returned 0 hits. SAD (but it's stil OK).
HMM Profiling for Bacteria_71
===============================================
Reference ....................................: Lee modified, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: bacteria
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmp44m_axxt/Bacteria_71.hmm
Number of genes in HMM model .................: 71
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 2
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5/AA_gene_sequences.fa.0_log
Log file for thread 1 ........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5/AA_gene_sequences.fa.1_log
Number of raw hits ...........................: 1
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 1
HMM Profiling for Archaea_76
===============================================
Reference ....................................: Lee, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: archaea
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmp44m_axxt/Archaea_76.hmm
Number of genes in HMM model .................: 76
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 2
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5/AA_gene_sequences.fa.0_log
Log file for thread 1 ........................: /home/iaf/christian.hoffmann/tmp/tmp9mw3ega5/AA_gene_sequences.fa.1_log
Number of raw hits ...........................: 1
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 1
(anvio-master) christian.hoffmann@scm00:~/github/anvio/anvio/tests> anvi-import-functions -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -i sandbox/example_interpro_output.tsv -p interproscan
Gene functions ...............................: 273 function calls from 11 sources (Pfam, PIRSF, TIGRFAM, SUPERFAMILY, Hamap, ProSitePatterns,
ProSiteProfiles, Gene3D, SMART, PRINTS, Coils) for 48 unique gene calls has been added to the contigs
database.
(anvio-master) christian.hoffmann@scm00:~/github/anvio/anvio/tests> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -H sandbox/external_hmm_profile --just-do-it
Segmentation fault
### this one works
(anvio-master) christian.hoffmann@scm00:~/github/anvio/anvio/tests> sqlite3 /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db '.tables'
amino_acid_additional_data hmm_hits
collections_bins_info hmm_hits_in_splits
collections_info hmm_hits_info
collections_of_contigs kmer_contigs
collections_of_splits kmer_splits
contig_sequences nt_position_info
contigs_basic_info nucleotide_additional_data
gene_amino_acid_sequences scg_taxonomy
gene_functions self
genes_in_contigs splits_basic_info
genes_in_splits splits_taxonomy
genes_taxonomy taxon_names
### later steps all produce segmentation fault.
A. Murat Eren
Aug 25, 2020, 10:48:42 PM8/25/20
to Anvi'o
Can you please try to run hmmscan on a toy data without anvi'o?
Unfortunately it is very difficult to diagnose these problems from far :/ This is likely an issue with the operating system.
To view this discussion on the web visit https://groups.google.com/d/msgid/anvio/00b63d5c-d73f-4c18-b443-936d87b422f2n%40googlegroups.com.
c.hof...@usp.br
Aug 26, 2020, 10:49:19 AM8/26/20
to Anvi'o
Hello Meren,
hmmscan works (output all the way down bellow).
However, I think I may have narrowed down the problem.
The segfaults are not really consistent (see output bellow):
I can't get anvi-gen-contigs-database (and other scripts) to behave properly.
It is almost as if
anvi-gen-contigs-database is calling something, a dependency or a library, and it has two (maybe more?) options, and every time it just randomly select one of the options it has.
If
anvi-gen-contigs-database works, and it creates the contig.db, I can use it downstream, but then I eventually also get the same behavior:
sometimes, it works, sometimes it just shows segmentation fault (sometimes it seems like it worked, and ends up showing the segfault message at the end).
I saw this behavior happening for:
anvi-gen-contigs-database
anvi-run-hmms
anvi-db-info
(and I tried adding --debug on the above scripts... same behavior, but more output... ).
however, for:
anvi-profile
anvi-import-taxonomy-for-layers
anvi-mergealthough sometimes they throws the segfault directly, it seems a much rarer occurrence. Most often it seems like it runs, and just present segfault at the end:
* Happy 😇
✓ anvi-profile took 0:00:11.749114
Segmentation fault
or:
* t_genus (w/2 items)
* t_family (w/2 items)
* t_species (w/3 items)
* Happy ☘
Segmentation fault
And
anvi-import-functions
never seems to give segfaults.
Again, no python wizard here, but it doesn't seem to be an outside program (at least I can call version/help for them all from the command line), but something in they python is dealing with the code and dependencies/modules (isn't the conda env supposed to keep things nice and self-contained anyway?)
Hopefully these tests can help shed some light onto it.
Let me know what I need to do now and will do it.
Thanks!
Chris
### series of tests, running independently the program calls from ./run_mini_test.sh
### sometimes I try using different -num-threads, because it seemed it was related to the issue... but I'm not sure about that
cd ~/anvioTestOutput
export output_dir=/home/iaf/christian.hoffmann/anvioTestOutput/test-output
export files=/home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-gen-contigs-database -f $files/contigs.fa -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -L 1000 --project-name "Contigs DB for anvi'o mini self-test" --num-threads 1
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-gen-contigs-database -f $files/contigs.fa -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -L 1000 --project-name "Contigs DB for anvi'o mini self-test" --num-threads 24
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-gen-contigs-database -f $files/contigs.fa -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -L 1000 --project-name "Contigs DB for anvi'o mini self-test" --num-threads 1
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-gen-contigs-database -f $files/contigs.fa -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS5.db -L 1000 --project-name "Contigs DB for anvi'o mini self-test" --num-threads 1
Input FASTA file .............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB for anvi'o mini self-test
Description ..................................: No description is given
Num threads for gene calling .................: 1
Finding ORFs in contigs
===============================================
Genes ........................................: /home/iaf/christian.hoffmann/tmp/tmpbi59hsct/contigs.genes
Amino acid sequences .........................: /home/iaf/christian.hoffmann/tmp/tmpbi59hsct/contigs.amino_acid_sequences
Log file .....................................: /home/iaf/christian.hoffmann/tmp/tmpbi59hsct/00_log.txt
CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.
Result .......................................: Prodigal (v2.6.3) has identified 51 genes.
CONTIGS DB CREATE REPORT
===============================================
Split Length .................................: 1,000
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: False
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True
Contigs with at least one gene call ..........: 6 of 6 (100.0%)
Contigs database .............................: A new database, /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS5.db, has been created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (what anvi'o gave back) .: 1,620
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> ls test-output/
CONTIGS5.db contigs.fa contigs-reformat-report.txt SAMPLE-01.bam SAMPLE-01.bam.bai SAMPLE-02.bam SAMPLE-02.bam.bai SAMPLE-03.bam SAMPLE-03.bam.bai
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-gen-contigs-database -f $files/contigs.fa -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db -L 1000 --project-name "Contigs DB for anvi'o mini self-test" --num-threads 1
Input FASTA file .............................: /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB for anvi'o mini self-test
Description ..................................: No description is given
Num threads for gene calling .................: 1
Finding ORFs in contigs
===============================================
Genes ........................................: /home/iaf/christian.hoffmann/tmp/tmpwzmsq3pi/contigs.genes
Amino acid sequences .........................: /home/iaf/christian.hoffmann/tmp/tmpwzmsq3pi/contigs.amino_acid_sequences
Log file .....................................: /home/iaf/christian.hoffmann/tmp/tmpwzmsq3pi/00_log.txt
CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.
Result .......................................: Prodigal (v2.6.3) has identified 51 genes.
CONTIGS DB CREATE REPORT
===============================================
Split Length .................................: 1,000
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: False
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True
Contigs with at least one gene call ..........: 6 of 6 (100.0%)
Contigs database .............................: A new database, /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS.db, has been created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (what anvi'o gave back) .: 1,620
Segmentation fault
####### running on a contig.db that was created with no apparent errors:
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db --num-threads 1 --just-do-it
WARNING
===============================================
Previous entries for "Ribosomal_RNAs" is being removed from "hmm_hits_info,
hmm_hits, hmm_hits_in_splits, genes_in_contigs, gene_functions"
WARNING
===============================================
Previous entries for "Bacteria_71" is being removed from "hmm_hits_info,
hmm_hits, hmm_hits_in_splits, genes_in_contigs, gene_functions"
WARNING
===============================================
Previous entries for "Archaea_76" is being removed from "hmm_hits_info,
hmm_hits, hmm_hits_in_splits, genes_in_contigs, gene_functions"
WARNING
===============================================
Previous entries for "Protista_83" is being removed from "hmm_hits_info,
hmm_hits, hmm_hits_in_splits, genes_in_contigs, gene_functions"
Target found .................................: AA:GENE
Target found .................................: RNA:CONTIG
HMM Profiling for Ribosomal_RNAs
===============================================
Reference ....................................: Seemann T, https://github.com/tseemann/barrnap
Kind .........................................: Ribosomal_RNAs
Alphabet .....................................: RNA
Context ......................................: CONTIG
Domain .......................................: N/A
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmpjcmyqv6y/Ribosomal_RNAs.hmm
Number of genes in HMM model .................: 12
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: nhmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmp1ro2l74d
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmp1ro2l74d/RNA_contig_sequences.fa.0_log
Number of raw hits ...........................: 0
* The HMM source 'Ribosomal_RNAs' returned 0 hits. SAD (but it's stil OK).
HMM Profiling for Protista_83
===============================================
Reference ....................................: Delmont, http://merenlab.org/delmont-euk-scgs
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: eukarya
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmpjcmyqv6y/Protista_83.hmm
Number of genes in HMM model .................: 83
Noise cutoff term(s) .........................: -E 1e-25
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmpdzy71m4f
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmpdzy71m4f/AA_gene_sequences.fa.0_log
Number of raw hits ...........................: 0
* The HMM source 'Protista_83' returned 0 hits. SAD (but it's stil OK).
HMM Profiling for Bacteria_71
===============================================
Reference ....................................: Lee modified, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: bacteria
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmpjcmyqv6y/Bacteria_71.hmm
Number of genes in HMM model .................: 71
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmpdzy71m4f
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmpdzy71m4f/AA_gene_sequences.fa.0_log
Number of raw hits ...........................: 1
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 1
HMM Profiling for Archaea_76
===============================================
Reference ....................................: Lee, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: archaea
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmpjcmyqv6y/Archaea_76.hmm
Number of genes in HMM model .................: 76
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmpdzy71m4f
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmpdzy71m4f/AA_gene_sequences.fa.0_log
Number of raw hits ...........................: 1
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 1
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db --num-threads 1 --just-do-it
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS.db
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
DB Info (no touch)
===============================================
Database Path ................................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 18
DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o mini self-test
contigs_db_hash ..............................: hashf0356823
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
external_gene_calls ..........................: 0
external_gene_amino_acid_seqs ................: 0
skip_predict_frame ...........................: 0
splits_consider_gene_calls ...................: 1
scg_taxonomy_was_run .........................: 0
scg_taxonomy_database_version ................: None
creation_date ................................: 1598448487.69134
* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be
extremely careful.
AVAILABLE GENE CALLERS
===============================================
* 'prodigal' (51 gene calls)
AVAILABLE HMM SOURCES
===============================================
* 'Ribosomal_RNAs' (type: Ribosomal_RNAs; num genes: 12)
* 'Protista_83' (type: singlecopy; num genes: 83)
* 'Bacteria_71' (type: singlecopy; num genes: 71)
* 'Archaea_76' (type: singlecopy; num genes: 76)
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
DB Info (no touch)
===============================================
Database Path ................................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 18
DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o mini self-test
contigs_db_hash ..............................: hashf0356823
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
external_gene_calls ..........................: 0
external_gene_amino_acid_seqs ................: 0
skip_predict_frame ...........................: 0
splits_consider_gene_calls ...................: 1
scg_taxonomy_was_run .........................: 0
scg_taxonomy_database_version ................: None
creation_date ................................: 1598448487.69134
* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be
extremely careful.
AVAILABLE GENE CALLERS
===============================================
* 'prodigal' (51 gene calls)
AVAILABLE HMM SOURCES
===============================================
* 'Ribosomal_RNAs' (type: Ribosomal_RNAs; num genes: 12)
* 'Protista_83' (type: singlecopy; num genes: 83)
* 'Bacteria_71' (type: singlecopy; num genes: 71)
* 'Archaea_76' (type: singlecopy; num genes: 76)
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
DB Info (no touch)
===============================================
Database Path ................................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 18
DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o mini self-test
contigs_db_hash ..............................: hashf0356823
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
external_gene_calls ..........................: 0
external_gene_amino_acid_seqs ................: 0
skip_predict_frame ...........................: 0
splits_consider_gene_calls ...................: 1
scg_taxonomy_was_run .........................: 0
scg_taxonomy_database_version ................: None
creation_date ................................: 1598448487.69134
* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be
extremely careful.
AVAILABLE GENE CALLERS
===============================================
* 'prodigal' (51 gene calls)
AVAILABLE HMM SOURCES
===============================================
* 'Ribosomal_RNAs' (type: Ribosomal_RNAs; num genes: 12)
* 'Protista_83' (type: singlecopy; num genes: 83)
* 'Bacteria_71' (type: singlecopy; num genes: 71)
* 'Archaea_76' (type: singlecopy; num genes: 76)
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
DB Info (no touch)
===============================================
Database Path ................................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 18
DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o mini self-test
contigs_db_hash ..............................: hashf0356823
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
external_gene_calls ..........................: 0
external_gene_amino_acid_seqs ................: 0
skip_predict_frame ...........................: 0
splits_consider_gene_calls ...................: 1
scg_taxonomy_was_run .........................: 0
scg_taxonomy_database_version ................: None
creation_date ................................: 1598448487.69134
* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be
extremely careful.
AVAILABLE GENE CALLERS
===============================================
* 'prodigal' (51 gene calls)
AVAILABLE HMM SOURCES
===============================================
* 'Ribosomal_RNAs' (type: Ribosomal_RNAs; num genes: 12)
* 'Protista_83' (type: singlecopy; num genes: 83)
* 'Bacteria_71' (type: singlecopy; num genes: 71)
* 'Archaea_76' (type: singlecopy; num genes: 76)
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
DB Info (no touch)
===============================================
Database Path ................................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 18
DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o mini self-test
contigs_db_hash ..............................: hashf0356823
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
external_gene_calls ..........................: 0
external_gene_amino_acid_seqs ................: 0
skip_predict_frame ...........................: 0
splits_consider_gene_calls ...................: 1
scg_taxonomy_was_run .........................: 0
scg_taxonomy_database_version ................: None
creation_date ................................: 1598448487.69134
* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be
extremely careful.
AVAILABLE GENE CALLERS
===============================================
* 'prodigal' (51 gene calls)
AVAILABLE HMM SOURCES
===============================================
* 'Ribosomal_RNAs' (type: Ribosomal_RNAs; num genes: 12)
* 'Protista_83' (type: singlecopy; num genes: 83)
* 'Bacteria_71' (type: singlecopy; num genes: 71)
* 'Archaea_76' (type: singlecopy; num genes: 76)
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-db-info $output_dir/CONTIGS6.db
Segmentation fault
###### anvi-import-functions tests
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-import-functions -c $output_dir/CONTIGS.db -i $files/example_interpro_output.tsv -p interproscan
Gene functions ...............................: 273 function calls from 11 sources (PRINTS, TIGRFAM, SUPERFAMILY, ProSitePatterns, PIRSF, Gene3D, Hamap, Coils, SMART, Pfam,
ProSiteProfiles) for 48 unique gene calls has been added to the contigs database.
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-import-functions -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -i $files/example_interpro_output.tsv -p interproscan
Gene functions ...............................: 273 function calls from 11 sources (Pfam, Gene3D, PIRSF, PRINTS, TIGRFAM, SUPERFAMILY, ProSiteProfiles, SMART, Coils,
ProSitePatterns, Hamap) for 48 unique gene calls has been added to the contigs database.
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-import-functions -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -i $files/example_interpro_output.tsv -p interproscan
WARNING
===============================================
Some of the annotation sources you want to add into the database are already in
the db. So anvi'o will REPLACE those with the incoming data from these sources:
Hamap, ProSiteProfiles, PRINTS, Gene3D, Coils, TIGRFAM, PIRSF, SMART,
SUPERFAMILY, Pfam, ProSitePatterns
Gene functions ...............................: 273 function calls from 11 sources (Hamap, ProSiteProfiles, PRINTS, Gene3D, Coils, TIGRFAM, PIRSF, SMART, ProSitePatterns,
SUPERFAMILY, Pfam) for 48 unique gene calls has been added to the contigs database.
#### hmm with external profile
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c $output_dir/CONTIGS.db -H $files/external_hmm_profile --just-do-it
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c $output_dir/CONTIGS.db -H $files/external_hmm_profile --just-do-it
HMM profiles .................................: 1 source been loaded: external_hmm_profile (2 genes)
Target found .................................: AA:GENE
HMM Profiling for external_hmm_profile
===============================================
Reference ....................................: Anvio et al, http://merenlab.org/projects/anvio
Kind .........................................: external_hmm_genes
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: N/A
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmpf1_c_v6s/external_hmm_profile.hmm
Number of genes in HMM model .................: 2
Noise cutoff term(s) .........................: -E 1e-12
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmpwtemymy6
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmpwtemymy6/AA_gene_sequences.fa.0_log
Number of raw hits ...........................: 4
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 4
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c $output_dir/CONTIGS.db -H $files/external_hmm_profile --just-do-it
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -H /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/external_hmm_profile/ --just-do-it
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -H /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/external_hmm_profile/ --just-do-it
HMM profiles .................................: 1 source been loaded: external_hmm_profile (2 genes)
Target found .................................: AA:GENE
HMM Profiling for external_hmm_profile
===============================================
Reference ....................................: Anvio et al, http://merenlab.org/projects/anvio
Kind .........................................: external_hmm_genes
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: N/A
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmp1bq3dgqu/external_hmm_profile.hmm
Number of genes in HMM model .................: 2
Noise cutoff term(s) .........................: -E 1e-12
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmpijgdkfzs
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmpijgdkfzs/AA_gene_sequences.fa.0_log
Number of raw hits ...........................: 4
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 4
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -H /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/external_hmm_profile/ --just-do-it --num-threads 1
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -H /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/external_hmm_profile/ --just-do-it --num-threads 1
Segmentation fault
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-run-hmms -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db -H /home/iaf/christian.hoffmann/github/anvio/anvio/tests/sandbox/external_hmm_profile/ --just-do-it --num-threads 1
HMM profiles .................................: 1 source been loaded: external_hmm_profile (2 genes)
WARNING
===============================================
Previous entries for "external_hmm_profile" is being removed from
"hmm_hits_info, hmm_hits, hmm_hits_in_splits, genes_in_contigs, gene_functions"
Target found .................................: AA:GENE
HMM Profiling for external_hmm_profile
===============================================
Reference ....................................: Anvio et al, http://merenlab.org/projects/anvio
Kind .........................................: external_hmm_genes
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: N/A
HMM model path ...............................: /home/iaf/christian.hoffmann/tmp/tmpvibetvad/external_hmm_profile.hmm
Number of genes in HMM model .................: 2
Noise cutoff term(s) .........................: -E 1e-12
Number of CPUs will be used for search .......: 1
HMMer program used for search ................: hmmscan
Temporary work dir ...........................: /home/iaf/christian.hoffmann/tmp/tmp55i5q9qy
Log file for thread 0 ........................: /home/iaf/christian.hoffmann/tmp/tmp55i5q9qy/AA_gene_sequences.fa.0_log
Number of raw hits ...........................: 4
Number of weak hits removed ..................: 0
Number of hits in annotation dict ...........: 4
#### seqlite3 cmd
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> sqlite3 $output_dir/CONTIGS.db '.tables'
amino_acid_additional_data hmm_hits
collections_bins_info hmm_hits_in_splits
collections_info hmm_hits_info
collections_of_contigs kmer_contigs
collections_of_splits kmer_splits
contig_sequences nt_position_info
contigs_basic_info nucleotide_additional_data
gene_amino_acid_sequences scg_taxonomy
gene_functions self
genes_in_contigs splits_basic_info
genes_in_splits splits_taxonomy
genes_taxonomy taxon_names
#### anvi-profile
same thing happens here, somethings just throws segfault, but it seems more often it runs as this:
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> anvi-profile -W -i /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03.bam -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03 -c $output_dir/CONTIGS6.db --cluster --profile-SCVs
Contigs DB .........................: Initialized: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db (v. 18)
anvio ..............................: 6.2-master
profiler_version ...................: 34
sample_id ..........................: SAMPLE_03
description ........................: None
profile_db .........................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03/PROFILE.db
contigs_db .........................: True
contigs_db_hash ....................: hashf0356823
cmd_line ...........................: /home/iaf/christian.hoffmann/github/anvio/bin/anvi-profile -W -i /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03.bam -o /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03 -c /home/iaf/christian.hoffmann/anvioTestOutput/test-output/CONTIGS6.db --cluster --profile-SCVs
merged .............................: False
blank ..............................: False
split_length .......................: 1,000
min_contig_length ..................: 1,000
max_contig_length ..................: 9,223,372,036,854,775,807
min_mean_coverage ..................: 0
clustering_performed ...............: True
min_coverage_for_variability .......: 10
skip_SNV_profiling .................: False
skip_INDEL_profiling ...............: False
profile_SCVs .......................: True
min_percent_identity ...............: None
report_variability_full ............: False
WARNING
=====================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.
input_bam ..........................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03.bam
output_dir .........................: /home/iaf/christian.hoffmann/anvioTestOutput/test-output/SAMPLE-03
num_reads_in_bam ...................: 24,870
num_contigs ........................: 3
num_contigs_after_M ................: 3
num_splits .........................: 35
total_length .......................: 56,709
New data for 'layers' in data group 'default'
=====================================
Data key "total_reads_mapped" ......: Predicted type: int
Data key "num_SNVs_reported" .......: Predicted type: int
Data key "total_reads_kept" ........: Predicted type: int
NEW DATA
=====================================
Database ...........................: profile
Data group .........................: default
Data table .........................: layers
New data keys ......................: total_reads_mapped, num_SNVs_reported, total_reads_kept.
New items order ....................: "tnf:euclidean:ward" (type newick) has been added to the database...
New items order ....................: "tnf-ab-cov:euclidean:ward" (type newick) has been added to the database...
* Happy 😇
✓ anvi-profile took 0:00:11.749114
Segmentation fault
##### HMMSCAN test
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> which hmmscan
/home/iaf/christian.hoffmann/miniconda3/envs/anvio-master/bin/hmmscan
(anvio-master) christian.hoffmann@scm01:~/anvioTestOutput> hmmscan -h
# hmmscan :: search sequence(s) against a profile database
# HMMER 3.3 (Nov 2019); http://hmmer.org/
(anvio-master) christian.hoffmann@scm00:~/anvioTestOutput/tutorial3.3> cat globins4.hmm fn3.hmm Pkinase.hmm > minifam
(anvio-master) christian.hoffmann@scm00:~/anvioTestOutput/tutorial3.3> hmmpress minifam
Working... done.
Pressed and indexed 3 HMMs (3 names and 2 accessions).
Models pressed into binary file: minifam.h3m
SSI index for binary model file: minifam.h3i
Profiles (MSV part) pressed into: minifam.h3f
Profiles (remainder) pressed into: minifam.h3p
(anvio-master) christian.hoffmann@scm00:~/anvioTestOutput/tutorial3.3> hmmscan minifam 7LESS_DROME
# hmmscan :: search sequence(s) against a profile database
# HMMER 3.3 (Nov 2019); http://hmmer.org/
# Copyright (C) 2019 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: 7LESS_DROME
# target HMM database: minifam
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: 7LESS_DROME [L=2554]
Accession: P13368
Description: RecName: Full=Protein sevenless; EC=2.7.10.1;
Scores for complete sequence (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Model Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
5.6e-57 178.0 0.4 3.5e-16 47.2 0.9 9.4 9 fn3 Fibronectin type III domain
1.1e-43 137.2 0.0 1.7e-43 136.5 0.0 1.3 1 Pkinase Protein kinase domain
Domain annotation for each model (and alignments):
>> fn3 Fibronectin type III domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -1.3 0.0 0.33 0.5 61 74 .. 396 409 .. 395 411 .. 0.85
2 ! 40.7 0.0 2.6e-14 3.8e-14 2 84 .. 439 520 .. 437 521 .. 0.95
3 ! 14.4 0.0 4.1e-06 6.1e-06 13 85 .. 836 913 .. 826 914 .. 0.73
4 ! 5.1 0.0 0.0032 0.0048 10 36 .. 1209 1235 .. 1203 1259 .. 0.82
5 ! 24.3 0.0 3.4e-09 5e-09 14 80 .. 1313 1380 .. 1304 1386 .. 0.82
6 ? 0.0 0.0 0.13 0.19 58 72 .. 1754 1768 .. 1739 1769 .. 0.89
7 ! 47.2 0.9 2.3e-16 3.5e-16 1 85 [. 1799 1890 .. 1799 1891 .. 0.91
8 ! 17.8 0.0 3.7e-07 5.5e-07 6 74 .. 1904 1966 .. 1901 1976 .. 0.90
9 ! 12.8 0.0 1.3e-05 2e-05 1 86 [] 1993 2107 .. 1993 2107 .. 0.89
Alignments for each domain:
== domain 1 score: -1.3 bits; conditional E-value: 0.33
EES--TT-EEEEEE CS
fn3 61 ltgLepgteYefrV 74
l+ L p+t+Y+fr
7LESS_DROME 396 LEALIPYTQYRFRF 409
67899*******95 PP
== domain 2 score: 40.7 bits; conditional E-value: 2.6e-14
---CEEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTEE-E CS
fn3 2 saPenlsvsevtstsltlsWsppkdgggpitgYeveyqekgegeewqevtvprtttsvtltgLepgteYefrVqavngagegp 84
saP ++ + ++ l ++W p + +gpi+gY++++++++++ + e+ vp+ s+ +++L++gt+Y++ + +n++gegp
7LESS_DROME 439 SAPVIEHLMGLDDSHLAVHWHPGRFTNGPIEGYRLRLSSSEGNA-TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGEGP 520
78999999999*****************************9998.**********************************9997 PP
== domain 3 score: 14.4 bits; conditional E-value: 4.1e-06
CTTEEEEEEE--S.--SS--S.....EEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTE.E-EB CS
fn3 13 tstsltlsWsppk.dgggpit.....gYeveyqekgegeewqevtvprtttsvtltgLepgteYefrVqavngag.egpe 85
++ + +sW++p+ ++ + + +Ye+e+ ++ ++++ +++ ++ + l+ L+p+ Y++rV+a+n +g g++
7LESS_DROME 836 GAQAAKISWKEPErNPYQSADaarswSYELEVLDVASQSAFSIRNIRGPI--FGLQRLQPDNLYQLRVRAINVDGePGEW 913
56677889999987443333223333899999999999955555566666..**********************965655 PP
== domain 4 score: 5.1 bits; conditional E-value: 0.0032
EEECTTEEEEEEE--S--SS--SEEEE CS
fn3 10 sevtstsltlsWsppkdgggpitgYev 36
++ + ++++W+p+++gg + ++Y++
7LESS_DROME 1209 DDGHWDDFHVRWQPSTSGGNHSVSYRL 1235
555678999*******99999999997 PP
== domain 5 score: 24.3 bits; conditional E-value: 3.4e-09
TTEEEEEEE--S...--SS--SEEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEEEEEETT CS
fn3 14 stsltlsWsppk...dgggpitgYeveyqekgegeewqevtvprtttsvtltgLepgteYefrVqavnga 80
+ s++l+W++p+ + + + Y + ++ ++ + e ++ ++ ++ +++L+p+++Y+f+V+a+ +a
7LESS_DROME 1313 NVSAVLRWDAPEqgqEAPMQALEYHISCWVG-SEL-HEELRLNQSALEARVEHLQPDQTYHFQVEARVAA 1380
5689********76556667899******55.665.688888888888*****************98665 PP
== domain 6 score: 0.0 bits; conditional E-value: 0.13
EEEEES--TT-EEEE CS
fn3 58 svtltgLepgteYef 72
s++lt+L p t+Y++
7LESS_DROME 1754 SLNLTDLLPFTRYRV 1768
799**********98 PP
== domain 7 score: 47.2 bits; conditional E-value: 2.3e-16
----CEEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCC.......GCEEEEEETTTSEEEEES--TT-EEEEEEEEEETTEE-EB CS
fn3 1 psaPenlsvsevtstsltlsWsppkdgggpitgYeveyqekgege.......ewqevtvprtttsvtltgLepgteYefrVqavngagegpe 85
ps+P+n+sv+ ++++l++sW pp++ +++ ++Y++++q++ +ge ++ + ++ +t+ ++ ltg++pg+ Y+++Vqa+ + +++ +
7LESS_DROME 1799 PSPPRNFSVRVLSPRELEVSWLPPEQLRSESVYYTLHWQQELDGEnvqdrreWEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNS 1890
9*************************************99989998****97777777777777*******************988776665 PP
== domain 8 score: 17.8 bits; conditional E-value: 3.7e-07
EEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCCGCEEEEEETTTSEEEEES--TT-EEEEEE CS
fn3 6 nlsvsevtstsltlsWsppkdgggpitgYeveyqekgegeewqevtvprtttsvtltgLepgteYefrV 74
+l++ e ++ sl+l+W +p+ + ++e++++ e+ +++v +++t ++++ L+p t+Y+ r+
7LESS_DROME 1904 ELQLLELGPYSLSLTWAGT---PDPLGSLQLECRSSAEQ---LRRNVAGNHTKMVVEPLQPRTRYQCRL 1966
5788899************...8***********88555...79**********************986 PP
== domain 9 score: 12.8 bits; conditional E-value: 1.3e-05
----CEEEEEEECTTEEEEEEE--S--SS--SEEEEEEEETTTCC...........................GCEEEEEETTTS.EEEEES--TT- CS
fn3 1 psaPenlsvsevtstsltlsWsppkdgggpitgYeveyqekgege...........................ewqevtvprttt.svtltgLepgt 68
ps+P+ ++++ + + ++++W++ + +g+pi Y++e + ++ e+q+ + +tt+ s+ ++ L ++
7LESS_DROME 1993 PSQPGKPQLEHIAEEVFRVTWTAARGNGAPIALYNLEALQARSDIrrrrrrrrrnsggsleqlpwaeepvvvEDQWLDFCNTTElSCIVKSLHSSR 2088
89***********************9************7775554799999999999999999999999999999999999999999999999999 PP
EEEEEEEEEETTE.E-EBE CS
fn3 69 eYefrVqavngag.egpes 86
frV+a++ + +gp+s
7LESS_DROME 2089 LLLFRVRARSLEHgWGPYS 2107
9999999999554488876 PP
>> Pkinase Protein kinase domain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 136.5 0.0 1.1e-43 1.7e-43 2 256 .. 2210 2479 .. 2209 2482 .. 0.85
Alignments for each domain:
== domain 1 score: 136.5 bits; conditional E-value: 1.1e-43
EEEEEEEEETTEEEEEEEETTTTE....EEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHH... CS
Pkinase 2 elleklGsGsfGkVykakkkktgk....kvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllk... 90
+ll+ lGsG+fG+Vy+++ k++ + +vA+K l+k ++ + +E++++ +++H+niv l++++ + +++ l++e++e+gdl ++l+
7LESS_DROME 2210 KLLRFLGSGAFGEVYEGQLKTEDSeepqRVAIKSLRKGASEFAELL---QEAQLMSNFKHENIVCLVGICFDTESISLIMEHMEAGDLLSYLRaar 2302
67899*********88776655444444********9998887764...4*******************************************998 PP
........HHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE.......EE--GTT.E..EECSS-C-S--S..-GGGS-HHH CS
Pkinase 91 ........kegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev.......kiaDFGlakkleksseklttlvg..treYmAPEv 169
ls e+ ++ +++g +yl +++++HrDL N+L++++ ki DFGla+ ++ks+ ++ g ++m+PE
7LESS_DROME 2303 atstqepqPTAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTESTGStdrrrtvKIGDFGLARDIYKSDYYRKEGEGllPVRWMSPES 2398
8887766555666************************************9554445999*************988887777766622679****** PP
HCCS-CTHHHHHHHHHHHHHHHHHH.SS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHT CS
Pkinase 170 llkakeytkkvDvWslGvilyellt.gklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilk 256
l + t+++DvW++Gv+++e+lt g+ p+ + ++ e++++++++ ++ p ++ e+l +l+ ++++dp +R++++++++
7LESS_DROME 2399 LV-DGLFTTQSDVWAFGVLCWEILTlGQQPYAAR---NNFEVLAHVKEGGRLQQ-PPMCT--EKLYSLLLLCWRTDPWERPSFRRCYN 2479
**.9999***************999899999999...55666655555443333.33344..89*******************99887 PP
Internal pipeline statistics summary:
-------------------------------------
Query sequence(s): 1 (2554 residues searched)
Target model(s): 3 (495 nodes)
Passed MSV filter: 2 (0.666667); expected 0.1 (0.02)
Passed bias filter: 2 (0.666667); expected 0.1 (0.02)
Passed Vit filter: 2 (0.666667); expected 0.0 (0.001)
Passed Fwd filter: 2 (0.666667); expected 0.0 (1e-05)
Initial search space (Z): 3 [actual number of targets]
Domain search space (domZ): 2 [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.03
# Mc/sec: 39.07
//
[ok]
c.hof...@usp.br
Aug 28, 2020, 10:01:30 AM8/28/20
to Anvi'o
Dear Meren et al,
I had a little chat with the system admin here and the system in this cluster I was working on is just too old.
I'm migrating to a new top node/cluster and I am glad to report: installation of the master branch was a success, and just using the default instruction.
And mini test finished with no problems (I have an issue on the full test, but I'll open a new topic on that).
I'll post the old system config here and the new one just to have a record.
Thanks for all you time, I'm happy to get Anvi'o working now.
Chris
## New system, where things are working:
> lsb_release -a
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.8.2003 (Core)
Release: 7.8.2003
Codename: Core
## old server
> lsb_release -a
LSB Version: core-2.0-noarch:core-3.2-noarch:core-4.0-noarch:core-2.0-x86_64:core-3.2-x86_64:core-4.0-x86_64:desktop-4.0-amd64:desktop-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:graphics-3.2-amd64:graphics-3.2-noarch:graphics-4.0-amd64:graphics-4.0-noarch
Distributor ID: SUSE LINUX
Description: SUSE Linux Enterprise Server 11 (x86_64)
Release: 11
Codename: n/a
> uname -r
3.0.13-0.27-default
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