Wanamalauasha
commented
2 years ago Hi! I run into the same problem!
Did you debug it somehow?
I run civet with the example config yaml file, which contains:
output_prefix: cluster_of_interest #defines the directory name that results will be put into
input_metadata: input_data/input_metadata.csv #path to input metadata csv
input_sequences: input_data/input_sequences.fasta #path to sequences we are adding in
datadir: background_data #data directory name
background_tree: background_data/background_tree.tree #background tree that will be searched
background_sequences: background_data/background_fasta.fasta #sequences corresponding to the tree
background_metadata: background_data/background_metadata.csv #metadata corresponding to the tree
tree_annotations: HCW_status,ward #fields to display on the phylogenies with
threads: 8And just run the following code:
civet -c config.yaml
Btw, here is my conda env:
# packages in environment at /home/seqadmin/anaconda3/envs/civet3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
amply 0.1.4 py_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
biopython 1.79 py39h3811e60_1 conda-forge
brotlipy 0.7.0 py39h3811e60_1003 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2021.10.8 py39hf3d152e_1 conda-forge
cffi 1.15.0 py39h4bc2ebd_0 conda-forge
charset-normalizer 2.0.10 pyhd8ed1ab_0 conda-forge
civet 3.0 pypi_0 pypi
coincbc 2.10.5 hcee13e7_1 conda-forge
configargparse 1.5.3 pyhd8ed1ab_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
constellations 0.1.2 pypi_0 pypi
cryptography 36.0.1 py39h95dcef6_0 conda-forge
cycler 0.11.0 pypi_0 pypi
datrie 0.8.2 py39h3811e60_3 conda-forge
docutils 0.18.1 py39hf3d152e_0 conda-forge
filelock 3.4.2 pyhd8ed1ab_1 conda-forge
fontconfig 2.13.94 ha180cfb_0 conda-forge
fonttools 4.29.0 pypi_0 pypi
freetype 2.10.4 h0708190_1 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gitdb 4.0.9 pyhd8ed1ab_0 conda-forge
gitpython 3.1.26 pyhd8ed1ab_0 conda-forge
gofasta 1.0.0 h9ee0642_0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
harfbuzz 2.9.1 h83ec7ef_1 conda-forge
icu 68.2 h9c3ff4c_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.10.1 py39hf3d152e_0 conda-forge
importlib_resources 5.4.0 pyhd8ed1ab_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
iqtree 2.2.0_beta hdcc8f71_0 bioconda
jbig 2.1 h7f98852_2003 conda-forge
jclusterfunk 0.0.25 1 cov-ert
jpeg 9e h7f98852_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.1 py39hf3d152e_1 conda-forge
k8 0.2.5 h9a82719_1 bioconda
kiwisolver 1.3.2 pypi_0 pypi
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libdeflate 1.8 h7f98852_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_12 conda-forge
libgfortran-ng 11.2.0 h69a702a_12 conda-forge
libgfortran5 11.2.0 h5c6108e_12 conda-forge
libglib 2.70.2 h174f98d_1 conda-forge
libgomp 11.2.0 h1d223b6_12 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_12 conda-forge
libtiff 4.3.0 h6f004c6_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
mako 1.1.6 pypi_0 pypi
markupsafe 2.0.1 pypi_0 pypi
matplotlib 3.5.1 pypi_0 pypi
minimap2 2.24 h5bf99c6_0 bioconda
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h9c3ff4c_0 conda-forge
numpy 1.22.1 py39h91f2184_0 conda-forge
openjdk 11.0.9.1 h5cc2fde_1 conda-forge
openssl 1.1.1l h7f98852_0 conda-forge
packaging 21.3 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 conda-forge
pillow 9.0.0 pypi_0 pypi
pip 21.2.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
psutil 5.9.0 py39h3811e60_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulp 2.6.0 py39hf3d152e_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py39h3811e60_0 conda-forge
pysocks 1.7.1 py39hf3d152e_4 conda-forge
python 3.9.9 h62f1059_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pyyaml 6.0 py39h3811e60_3 conda-forge
ratelimiter 1.2.0 py_1002 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
scorpio 0.3.16 pypi_0 pypi
setuptools 60.5.0 py39hf3d152e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smart_open 5.2.1 pyhd8ed1ab_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snakemake-minimal 6.8.0 pyhdfd78af_0 bioconda
snipit 1.0.3 pypi_0 pypi
sqlite 3.37.0 h9cd32fc_0 conda-forge
stopit 1.1.2 py_0 conda-forge
tabulate 0.8.9 pyhd8ed1ab_0 conda-forge
tk 8.6.11 h27826a3_1 conda-forge
toposort 1.7 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typing_extensions 4.0.1 pyha770c72_0 conda-forge
tzdata 2021e he74cb21_0 conda-forge
urllib3 1.26.8 pyhd8ed1ab_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.13.3 py39h3811e60_1 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.7.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forgeCould it be a problem related to snipit or snakemake-minimal versions?
Thanks in advance @aineniamh @rambaut ! Looking forward to use this amazing tool!!
omarkr8
Running snipit pipeline. MissingInputException in line 68 of /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/snipit_runner.smk: Missing input files for rule gather_graphs: /tmp/tmppiy9q6qf/snipit/.snipit.svg [Mon Jan 17 16:46:59 2022] Error in rule snipit: jobid: 0 output: /tmp/tmppiy9q6qf/snipit/prompt.txt
RuleException: CalledProcessError in line 247 of /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/civet.smk: Command 'set -euo pipefail; snakemake --nolock --snakefile /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/snipit_runner.smk --forceall --quiet --log-handler-script /home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/utils/log_handler_handle.py --directory /tmp/tmppiy9q6qf --configfile /home/lab6/civet/civet/tests/file_test1_3/config.yaml --config fasta=/tmp/tmppiy9q6qf/hashed.aln.fasta csv=/home/lab6/civet/civet/tests/file_test1_3/master_metadata.csv --cores 1 && touch /tmp/tmppiy9q6qf/snipit/prompt.txt' returned non-zero exit status 1. File "/home/lab6/anaconda3/envs/civet/lib/python3.9/site-packages/civet/scripts/civet.smk", line 247, in __rule_snipit File "/home/lab6/anaconda3/envs/civet/lib/python3.9/concurrent/futures/thread.py", line 58, in run Exiting because a job execution failed. Look above for error message Exiting because a job execution failed. Look above for error message
achieved by running this code :
civet --input-metadata imr6_1/background_metadata.csv \ --input-sequences imr6_1/background_sequences.aln.fasta \ --timeline-dates sample_date \ --datadir gisomi_1/ \ -bseq gisomi_1/background_sequences.aln.fasta \ -bm gisomi_1/background_metadata.csv \ -bicol sequence_header -icol sequence_header \ -ta country --outdir file_test1 \ --snp-distance 100 -ds mode=normalise country -n 0.1