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snipit error, not sure how to debug #149

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omarkr8 opened this issue Jan 17, 2022 · 2 comments
Open

snipit error, not sure how to debug #149

omarkr8 opened this issue Jan 17, 2022 · 2 comments

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@omarkr8
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omarkr8 commented Jan 17, 2022

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

@Wanamalauasha
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Wanamalauasha commented Feb 21, 2022

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: 8

And 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-forge

Could it be a problem related to snipit or snakemake-minimal versions?

Thanks in advance @aineniamh @rambaut ! Looking forward to use this amazing tool!!

@omarkr8
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omarkr8 commented Apr 5, 2022

Not sure what triggered it still,
but i am no longer experiencing issues and am able to generate nice reports :)

I did start over from background generation from an alignment. Many thanks

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