First test - missing spec-file.txt for plasflow installation
Heres my output for the very first test. Running conda 4.7.5 on the server. It seems that plasflow cannot be installed ('missing file spec-file.txt').
Hope this helps!
Anita
(snakemake) anita@VM012073:~/gplas-TESTING$ git clone https://gitlab.com/sirarredondo/gplas.git
Cloning into 'gplas'...
Username for 'https://gitlab.com': anita.schuerch@gmail.com
Password for 'https://anita.schuerch@gmail.com@gitlab.com':
remote: Enumerating objects: 64, done.
remote: Counting objects: 100% (64/64), done.
remote: Compressing objects: 100% (37/37), done.
remote: Total 64 (delta 28), reused 57 (delta 25)
Unpacking objects: 100% (64/64), done.
Checking connectivity... done.
(snakemake) anita@VM012073:~/gplas-TESTING$ cd gplas/
(snakemake) anita@VM012073:~/gplas-TESTING/gplas$ ls
config.yaml envs final.yaml final.yml gplas.sh mlplasmidssnake.smk plasflowsnake.smk README.md README.Rmd scripts template.yml temp.yaml temp.yml test
(snakemake) anita@VM012073:~/gplas-TESTING/gplas$ ./gplas.sh -i test/faecium_graph.gfa
!!!!!!Welcome to GPLAS!!!!!!
####### Preparation of the files for snakemake #########################
This is your INPUT graph: test/faecium_graph.gfa
You have not indicated the SPECIES that you are trying to predict. Your genome will be considered as a METAGENOME and predicted by plasflow
Plasmid prediction will be perfomed using plasflow
You have not passed the NAME of the project. Your results will be named as 'unnamed_project''
You have not passed a minimum threshold to carry out the plasmid prediction, using 0.5 as default
You have not passed the number of times to look for paths based on each plasmid seed, using 10 as default
##################################################################
samples:
"unnamed_project": "test/faecium_graph.gfa"
species: "metagenome"
threshold_prediction: "0.5"
number_iterations: "10"
classifier: "plasflow"
Conda is present, so there is no need to install it. Well done!
Let's check if snakemake is present in a previous conda environment, otherwise will proceed to the installation
CondaEnvironmentNotFoundError: Could not find environment: snakeplas .
You can list all discoverable environments with `conda info --envs`.
Fetching package metadata ...............
Solving package specifications: .
Package plan for installation in environment /home/anita/miniconda3/envs/snakemake/envs/snakeplas:
The following NEW packages will be INSTALLED:
_libgcc_mutex: 0.1-main
aioeasywebdav: 2.2.0-py35_0 conda-forge
aiohttp: 3.4.4-py35h470a237_0 conda-forge
appdirs: 1.4.3-py_1 conda-forge
asn1crypto: 0.24.0-py35_3 conda-forge
async-timeout: 3.0.1-py_1000 conda-forge
attrs: 19.1.0-py_0 conda-forge
bcrypt: 3.1.4-py35h14c3975_0
blas: 2.10-openblas conda-forge
boto3: 1.9.88-py_0 conda-forge
botocore: 1.12.185-py_0 conda-forge
bzip2: 1.0.6-h14c3975_1002 conda-forge
ca-certificates: 2019.6.16-hecc5488_0 conda-forge
cachetools: 2.1.0-py_0 conda-forge
cairo: 1.16.0-h18b612c_1001 conda-forge
certifi: 2018.8.24-py35_1001 conda-forge
cffi: 1.11.5-py35h5e8e0c9_1 conda-forge
chardet: 3.0.4-py35_3 conda-forge
configargparse: 0.13.0-py_1 conda-forge
cryptography: 2.3.1-py35hdffb7b8_0 conda-forge
cryptography-vectors: 2.3.1-py35_0 conda-forge
datrie: 0.7.1-py35h7b6447c_1
decorator: 4.4.0-py_0 conda-forge
docutils: 0.14-py35_1 conda-forge
dropbox: 9.4.0-py_0 conda-forge
expat: 2.2.5-he1b5a44_1003 conda-forge
filechunkio: 1.8-py_2 conda-forge
fontconfig: 2.13.1-he4413a7_1000 conda-forge
freetype: 2.10.0-he983fc9_0 conda-forge
ftputil: 3.4-py_0 conda-forge
futures: 3.0.3-py35_0
gettext: 0.19.8.1-hc5be6a0_1002 conda-forge
glib: 2.58.3-h6f030ca_1001 conda-forge
google-api-core: 1.7.0-py_0 conda-forge
google-auth: 1.6.3-py_0 conda-forge
google-cloud-core: 0.29.1-py_0 conda-forge
google-cloud-storage: 1.16.1-py_0 conda-forge
google-resumable-media: 0.3.2-py_0 conda-forge
googleapis-common-protos: 1.5.9-1 conda-forge
graphite2: 1.3.13-hf484d3e_1000 conda-forge
graphviz: 2.38.0-hf68f40c_1011 conda-forge
harfbuzz: 2.4.0-h37c48d4_1 conda-forge
icu: 58.2-hf484d3e_1000 conda-forge
idna: 2.7-py35_2 conda-forge
idna_ssl: 1.0.0-0 conda-forge
jinja2: 2.10.1-py_0 conda-forge
jmespath: 0.9.4-py_0 conda-forge
jpeg: 9c-h14c3975_1001 conda-forge
jsonschema: 2.6.0-py35_2 conda-forge
libblas: 3.8.0-10_openblas conda-forge
libcblas: 3.8.0-10_openblas conda-forge
libffi: 3.2.1-he1b5a44_1006 conda-forge
libgcc-ng: 9.1.0-hdf63c60_0
libgfortran-ng: 7.3.0-hdf63c60_0
libiconv: 1.15-h516909a_1005 conda-forge
liblapack: 3.8.0-10_openblas conda-forge
liblapacke: 3.8.0-10_openblas conda-forge
libopenblas: 0.3.6-h6e990d7_4 conda-forge
libpng: 1.6.37-hed695b0_0 conda-forge
libprotobuf: 3.6.0-hdbcaa40_1000 conda-forge
libstdcxx-ng: 9.1.0-hdf63c60_0
libtiff: 4.0.10-h57b8799_1003 conda-forge
libtool: 2.4.6-h14c3975_1002 conda-forge
libuuid: 2.32.1-h14c3975_1000 conda-forge
libxcb: 1.13-h14c3975_1002 conda-forge
libxml2: 2.9.9-h13577e0_1 conda-forge
lz4-c: 1.8.3-he1b5a44_1001 conda-forge
markupsafe: 1.0-py35h470a237_1 conda-forge
multidict: 4.4.2-py35h470a237_0 conda-forge
ncurses: 6.1-hf484d3e_1002 conda-forge
networkx: 2.3-py_0 conda-forge
numpy: 1.15.2-py35h99e49ec_0
numpy-base: 1.15.2-py35h2f8d375_0
openblas: 0.3.6-h6e990d7_4 conda-forge
openssl: 1.0.2r-h14c3975_0 conda-forge
pandas: 0.23.4-py35hf8a1672_0 conda-forge
pango: 1.40.14-he7ab937_1005 conda-forge
paramiko: 2.4.1-py35_0 conda-forge
pcre: 8.41-hf484d3e_1003 conda-forge
pip: 18.0-py35_1001 conda-forge
pixman: 0.38.0-h516909a_1003 conda-forge
prettytable: 0.7.2-py_3 conda-forge
protobuf: 3.6.0-py35hfc679d8_0 conda-forge
psutil: 5.4.7-py35h14c3975_1001 conda-forge
pthread-stubs: 0.4-h14c3975_1001 conda-forge
pyasn1: 0.4.5-py_0 conda-forge
pyasn1-modules: 0.2.5-py_0 conda-forge
pycparser: 2.19-py_0 conda-forge
pygraphviz: 1.4rc1-py35h470a237_0 conda-forge
pynacl: 1.1.2-py35_0 conda-forge
pyopenssl: 18.0.0-py35_0 conda-forge
pysftp: 0.2.9-py_1 conda-forge
pysocks: 1.6.8-py35_2 conda-forge
python: 3.5.5-h5001a0f_2 conda-forge
python-dateutil: 2.8.0-py_0 conda-forge
python-irodsclient: 0.7.0-py_0 conda-forge
pytz: 2019.1-py_0 conda-forge
pyyaml: 3.13-py35h470a237_1 conda-forge
ratelimiter: 1.2.0-py35_1000 conda-forge
readline: 7.0-hf8c457e_1001 conda-forge
requests: 2.19.1-py35_1 conda-forge
rsa: 3.4.2-py_1 conda-forge
s3transfer: 0.1.13-py35_1 conda-forge
setuptools: 40.4.3-py35_0 conda-forge
six: 1.11.0-py35_1 conda-forge
snakemake: 5.2.2-py35_1 bioconda
snakemake-minimal: 5.2.2-py35_1 bioconda
sqlite: 3.28.0-h8b20d00_0 conda-forge
tk: 8.6.9-hed695b0_1002 conda-forge
urllib3: 1.23-py35_1 conda-forge
wheel: 0.32.0-py35_1000 conda-forge
wrapt: 1.10.11-py35h470a237_1 conda-forge
xmlrunner: 1.7.7-py_0 conda-forge
xorg-kbproto: 1.0.7-h14c3975_1002 conda-forge
xorg-libice: 1.0.9-h516909a_1004 conda-forge
xorg-libsm: 1.2.3-h84519dc_1000 conda-forge
xorg-libx11: 1.6.7-h14c3975_1000 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: 3.5.12-h14c3975_1002 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: 5.2.4-h14c3975_1001 conda-forge
yaml: 0.1.7-h14c3975_1001 conda-forge
yarl: 1.2.6-py35h470a237_0 conda-forge
zlib: 1.2.11-h14c3975_1004 conda-forge
zstd: 1.4.0-h3b9ef0a_0 conda-forge
botocore-1.12. 100% |############################################################################################################################################################| Time: 0:00:00 4.68 MB/s
#
# To activate this environment, use:
# > source activate snakeplas
#
# To deactivate an active environment, use:
# > source deactivate
#
PlasFlow is missing. No worries, starting installation using the conda environment....
CondaFileIOError: 'spec-file.txt'. [Errno 2] No such file or directory: 'spec-file.txt'
Building DAG of jobs...
Creating conda environment envs/r_packages.yaml...
Downloading remote packages.
Environment for envs/r_packages.yaml created (location: .snakemake/conda/6cde993d)
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 awk_links
1 awk_nodes
1 gplas_coocurr
1 gplas_coverage
1 gplas_paths
1 plasflow
6
[Wed Jul 10 14:33:14 2019]
Job 5: Extracting the links from the graph test/faecium_graph.gfa
Activating conda environment: /home/anita/gplas-TESTING/gplas/.snakemake/conda/6cde993d
[Wed Jul 10 14:33:17 2019]
Finished job 5.
1 of 6 steps (17%) done
[Wed Jul 10 14:33:17 2019]
Job 1: Extracting the nodes from the graph test/faecium_graph.gfa
Activating conda environment: /home/anita/gplas-TESTING/gplas/.snakemake/conda/6cde993d
[Wed Jul 10 14:33:20 2019]
Finished job 1.
2 of 6 steps (33%) done
[Wed Jul 10 14:33:21 2019]
Job 3: Running plasflow to obtain the plasmid prediction using the nodes extracted from the graph
[Wed Jul 10 14:33:21 2019]
Error in rule plasflow:
jobid: 3
output: plasflow_prediction/unnamed_project_plasmid_prediction.tab
log: logs/unnamed_project_error_log_plasflow.txt, logs/unnamed_project_normal_log_plasflow.txt
RuleException:
CalledProcessError in line 45 of /home/anita/gplas-TESTING/gplas/plasflowsnake.smk:
Command ' set -euo pipefail; PlasFlow.py --input gplas_input/unnamed_project_raw_nodes.fasta --output plasflow_prediction/unnamed_project_plasmid_prediction.tab 1>> logs/unnamed_project_normal_log_plasflow.txt 2>> logs/unnamed_project_error_log_plasflow.txt ' returned non-zero exit status 127
File "/home/anita/gplas-TESTING/gplas/plasflowsnake.smk", line 45, in __rule_plasflow
File "/home/anita/miniconda3/envs/snakemake/envs/snakeplas/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/anita/gplas-TESTING/gplas/.snakemake/log/2019-07-10T142619.125888.snakemake.log
Seems like something went wrong!