Open JoeEmendo opened 6 years ago
JoeEmendo
commented
6 years ago this is the test.sh file (unchanged from original download)
set -e
echo "Testing CLI (usage should print)" ./disco.sh --help
echo "Testing CRISPRdisco test run" rm -Rf test/test_output/. ./disco.sh --workingdir test/temp_test_output --outdir test/test_output --refset typing --date TEST test/test_infile.csv
echo "Replication of CRISPRdisco output" diff -s test/known_results test/test_output
echo "Tests pass"
brinerallie
commented
6 years ago Hi Joe - Are you using CRISPRdisco in the Docker container or installed locally?
JoeEmendo
commented
6 years ago Hi, I'm using the docker. I think I follow your guidelines, maybe I miss something. Below is full list of commands after opening docker terminal.
## .
## ## ## ==
## ## ## ## ## ===
/"""""""""""""""""\___/ ===
~~~ {~~ ~~~~ ~~~ ~~~~ ~~~ ~ / ===- ~~~
\______ o __/
\ \ __/
\____\_______/docker is configured to use the default machine with IP 192.168.99.100 For help getting started, check out the docs at https://docs.docker.com
Joes-MacBook-Pro:~ joe$ git clone https://github.com/CRISPRlab/CRISPRdisco.git; cd CRISPRdisco fatal: destination path 'CRISPRdisco' already exists and is not an empty directory. Joes-MacBook-Pro:CRISPRdisco joe$ docker login Login with your Docker ID to push and pull images from Docker Hub. If you don't have a Docker ID, head over to https://hub.docker.com to create one. Username (joemg55345): Password: Login Succeeded Joes-MacBook-Pro:CRISPRdisco joe$ make setup Logged in to dockerhub. time docker build --rm -f Dockerfile -t crisprlab/crisprdisco . Sending build context to Docker daemon 65.96MB Step 1/8 : FROM continuumio/miniconda:4.1.11 ---> 23412a68e1b0 Step 2/8 : USER root ---> Using cache ---> f0cb778e9541 Step 3/8 : RUN apt-get update --fix-missing && apt-get install -y --no-install-recommends build-essential=11.7 && apt-get clean && apt-get autoremove && rm -rf /var/lib/apt/lists/ /tmp/ /var/tmp/ ---> Using cache ---> e05d56b5fe41 Step 4/8 : RUN conda install -y -c bioconda "python=2.7.12" "blast=2.6.0" "minced=0.2.0" "hmmer=3.1b2" "conda=4.1.11" && conda clean -i -l -t -y && rm -rf /tmp/ /var/tmp/* ---> Running in 1b488cb3636e Fetching package metadata ......... Solving package specifications: ..........
Package plan for installation in environment /opt/conda:
The following packages will be downloaded:
package | build
---------------------------|-----------------
hmmer-3.1b2 | 3 5.5 MB bioconda
icu-54.1 | 0 11.3 MB
libgcc-5.2.0 | 0 1.1 MB
openjdk-8.0.121 | 1 64.2 MB
minced-0.2.0 | 1 29 KB bioconda
boost-1.61.0 | py27_0 16.1 MB
blast-2.6.0 | boost1.61_1 245.6 MB bioconda
------------------------------------------------------------
Total: 343.8 MBThe following NEW packages will be INSTALLED:
blast: 2.6.0-boost1.61_1 bioconda
boost: 1.61.0-py27_0
hmmer: 3.1b2-3 bioconda
icu: 54.1-0
libgcc: 5.2.0-0
minced: 0.2.0-1 bioconda
openjdk: 8.0.121-1 Fetching packages ... hmmer-3.1b2-3. 100% |###############################| Time: 0:00:25 226.16 kB/skB/s icu-54.1-0.tar 100% |###############################| Time: 0:00:12 934.40 kB/s libgcc-5.2.0-0 100% |###############################| Time: 0:00:00 1.22 MB/s openjdk-8.0.12 100% |###############################| Time: 0:01:22 813.74 kB/s minced-0.2.0-1 100% |###############################| Time: 0:00:00 188.39 kB/s boost-1.61.0-p 100% |###############################| Time: 0:00:13 1.25 MB/s blast-2.6.0-bo 100% |###############################| Time: 0:07:41 558.13 kB/s Extracting packages ... [ COMPLETE ]|##################################################| 100% Linking packages ... [ COMPLETE ]|##################################################| 100% Cache location: /opt/conda/pkgs Will remove the following tarballs:
hmmer-3.1b2-3.tar.bz2 5.5 MB minced-0.2.0-1.tar.bz2 29 KB openjdk-8.0.121-1.tar.bz2 64.2 MB boost-1.61.0-py27_0.tar.bz2 16.1 MB libgcc-5.2.0-0.tar.bz2 1.1 MB icu-54.1-0.tar.bz2 11.3 MB blast-2.6.0-boost1.61_1.tar.bz2 245.6 MB
Total: 343.8 MB
Removing hmmer-3.1b2-3.tar.bz2 Removing minced-0.2.0-1.tar.bz2 Removing openjdk-8.0.121-1.tar.bz2 Removing boost-1.61.0-py27_0.tar.bz2 Removing libgcc-5.2.0-0.tar.bz2 Removing icu-54.1-0.tar.bz2 Removing blast-2.6.0-boost1.61_1.tar.bz2 Removing intermediate container 1b488cb3636e ---> bc92d9f801fc Step 5/8 : COPY . /opt/app ---> 67228104fec6 Step 6/8 : RUN cd /opt/app && pip install --disable-pip-version-check -e . && rm -rf /root/.cache/pip/* ---> Running in 8ba97b87b2e5 Obtaining file:///opt/app Collecting pandas==0.22.0 (from crisprdisco===development) Downloading https://files.pythonhosted.org/packages/6b/b5/76538d8a202f8c368d30c18892d33664d1a3b2c078af8513ee5b5d172629/pandas-0.22.0-cp27-cp27mu-manylinux1_x86_64.whl (24.3MB) Collecting numpy==1.14.0 (from crisprdisco===development) Downloading https://files.pythonhosted.org/packages/0d/8a/e0223a40f980e0442a2045dcf79e4a8a90339593525599a0add318da2428/numpy-1.14.0-cp27-cp27mu-manylinux1_x86_64.whl (16.9MB) Collecting biopython==1.70 (from crisprdisco===development) Downloading https://files.pythonhosted.org/packages/b5/9a/95e0cbac0104808b0e2f48dfeaafb1daf6cb5c711c3ec599af68663f2a71/biopython-1.70-cp27-cp27mu-manylinux1_x86_64.whl (2.2MB) Collecting click==6.7 (from crisprdisco===development) Downloading https://files.pythonhosted.org/packages/34/c1/8806f99713ddb993c5366c362b2f908f18269f8d792aff1abfd700775a77/click-6.7-py2.py3-none-any.whl (71kB) Collecting pytz>=2011k (from pandas==0.22.0->crisprdisco===development) Downloading https://files.pythonhosted.org/packages/dc/83/15f7833b70d3e067ca91467ca245bae0f6fe56ddc7451aa0dc5606b120f2/pytz-2018.4-py2.py3-none-any.whl (510kB) Collecting python-dateutil (from pandas==0.22.0->crisprdisco===development) Downloading https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl (211kB) Collecting six>=1.5 (from python-dateutil->pandas==0.22.0->crisprdisco===development) Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl Installing collected packages: pytz, numpy, six, python-dateutil, pandas, biopython, click, crisprdisco Running setup.py develop for crisprdisco Successfully installed biopython-1.70 click-6.7 crisprdisco numpy-1.14.0 pandas-0.22.0 python-dateutil-2.7.3 pytz-2018.4 six-1.11.0 Removing intermediate container 8ba97b87b2e5 ---> 5b3b6559c6b4 Step 7/8 : WORKDIR /home/crisprlab Removing intermediate container 5effe34d2b76 ---> 4b60552b99db Step 8/8 : ENTRYPOINT ["/usr/bin/tini", "--"] ---> Running in 4d418575447b Removing intermediate container 4d418575447b ---> 2bf2f867a6e2 Successfully built 2bf2f867a6e2 Successfully tagged crisprlab/crisprdisco:latest
real 14m16.830s user 0m0.336s sys 0m0.264s Joes-MacBook-Pro:CRISPRdisco joe$ docker ps CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES f774fea124c1 e05d56b5fe41 "/bin/sh -c 'conda i…" 9 hours ago Up 9 hours infallible_euler 7217bed1d924 e05d56b5fe41 "/bin/sh -c 'conda i…" 9 hours ago Up 9 hours heuristic_ritchie 4b71e0be56d2 e05d56b5fe41 "/bin/sh -c 'conda i…" 11 hours ago Up 11 hours affectionate_snyder Joes-MacBook-Pro:CRISPRdisco joe$ conda update conda Solving environment: done
Joes-MacBook-Pro:CRISPRdisco joe$ conda info
active environment : None
user config file : /Users/joe/.condarcpopulated config files : conda version : 4.5.4 conda-build version : not installed python version : 3.6.5.final.0 base environment : /Users/joe/miniconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/osx-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/osx-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /Users/joe/miniconda3/pkgs /Users/joe/.conda/pkgs envs directories : /Users/joe/miniconda3/envs /Users/joe/.conda/envs platform : osx-64 user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Darwin/17.4.0 OSX/10.13.3 UID:GID : 501:20 netrc file : None offline mode : False
Joes-MacBook-Pro:CRISPRdisco joe$ sh test.sh Testing CLI (usage should print) Usage: disco [OPTIONS] INFILE
INFILE is a csv file with a column called "Path" that has the full path to the genomes of #interest. Do not include file extensions in this column.
Options: --workingdir TEXT Path to working directory. Default = . --outdir TEXT Path to final directory. Default = . --refset [full|typing] full or subset for typing. Default = full --date TEXT Date of analysis in YYYY-MM-DD format. Default is today. --tax [no|yes] If "yes", will merge taxonomic information. Include columns titled "organism", "Taxonomic ID Kingdom", "Taxonomic ID Phylum", "Taxonomic ID Class", "Taxonomic ID Order", "Taxonomic ID Family", "Taxonomic ID Genus". "organism" should match the name of the file. --cas [T|F] Perform BLAST search. Default is True --evalue TEXT BLAST evalue. Default is 1e-6. --idcutoff INTEGER Minimum % identity to reference protein to be considered a positive hit. Default is 40%. --lengthcutoff INTEGER Minimum % coverage of reference protein to be considered a positive hit. Default is 50%. --repeats [T|F] Perform CRISPR repeat search. Default is True --summary [T|F] Generate master summary table with type analysis. Default is True. --dbsearch TEXT Provide the location of a protein database --prot TEXT Provide the protein to search for. --domains TEXT Provide the location of an HMM domain database that is already compiled --temp [delete|keep] Temporary files automatically deleted. Change to --temp keep to retain temporary files --help Show this message and exit.
real 0m1.063s
user 0m0.090s
sys 0m0.025s
Testing CRISPRdisco test run
Searching for Cas proteins
Searching using 31 reference sets
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_015847.faa.blastp'
Command line argument error: Argument "out". File is not accessible: test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp'
Traceback (most recent call last):
File "/opt/conda/bin/disco", line 9, in
real 0m3.451s user 0m0.098s sys 0m0.031s Joes-MacBook-Pro:CRISPRdisco joe$ docker info Containers: 14 Running: 3 Paused: 0 Stopped: 11 Images: 34 Server Version: 18.05.0-ce Storage Driver: aufs Root Dir: /mnt/sda1/var/lib/docker/aufs Backing Filesystem: extfs Dirs: 92 Dirperm1 Supported: true Logging Driver: json-file Cgroup Driver: cgroupfs Plugins: Volume: local Network: bridge host macvlan null overlay Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog Swarm: inactive Runtimes: runc Default Runtime: runc Init Binary: docker-init containerd version: 773c489c9c1b21a6d78b5c538cd395416ec50f88 runc version: 4fc53a81fb7c994640722ac585fa9ca548971871 init version: 949e6fa Security Options: seccomp Profile: default Kernel Version: 4.9.93-boot2docker Operating System: Boot2Docker 18.05.0-ce (TCL 8.2.1); HEAD : b5d6989 - Thu May 10 16:35:28 UTC 2018 OSType: linux Architecture: x86_64 CPUs: 1 Total Memory: 1.955GiB Name: default ID: WFWS:3FEX:254K:4L2W:GT3Q:WHXM:7GQS:673Y:SY4H:LIPS:OL2E:MJNN Docker Root Dir: /mnt/sda1/var/lib/docker Debug Mode (client): false Debug Mode (server): false Username: joemg55345 Registry: https://index.docker.io/v1/ Labels: provider=virtualbox Experimental: false Insecure Registries: 127.0.0.0/8 Live Restore Enabled: false
Joes-MacBook-Pro:CRISPRdisco joe$
Any idea what I'm doing wrong?
Joes-MacBook-Pro:CRISPRdisco joe$ sh test.sh Testing CLI (usage should print) Usage: disco [OPTIONS] INFILE
INFILE is a csv file with a column called "Path" that has the full path to the genomes of #interest. Do not include file extensions in this column.
Options: --workingdir TEXT Path to working directory. Default = . --outdir TEXT Path to final directory. Default = . --refset [full|typing] full or subset for typing. Default = full --date TEXT Date of analysis in YYYY-MM-DD format. Default is today. --tax [no|yes] If "yes", will merge taxonomic information. Include columns titled "organism", "Taxonomic ID Kingdom", "Taxonomic ID Phylum", "Taxonomic ID Class", "Taxonomic ID Order", "Taxonomic ID Family", "Taxonomic ID Genus". "organism" should match the name of the file. --cas [T|F] Perform BLAST search. Default is True --evalue TEXT BLAST evalue. Default is 1e-6. --idcutoff INTEGER Minimum % identity to reference protein to be considered a positive hit. Default is 40%. --lengthcutoff INTEGER Minimum % coverage of reference protein to be considered a positive hit. Default is 50%. --repeats [T|F] Perform CRISPR repeat search. Default is True --summary [T|F] Generate master summary table with type analysis. Default is True. --dbsearch TEXT Provide the location of a protein database --prot TEXT Provide the protein to search for. --domains TEXT Provide the location of an HMM domain database that is already compiled --temp [delete|keep] Temporary files automatically deleted. Change to --temp keep to retain temporary files --help Show this message and exit.
real 0m0.941s user 0m0.104s sys 0m0.024s Testing CRISPRdisco test run Searching for Cas proteins Searching using 31 reference sets Command line argument error: Argument "out". File is not accessible:
load_entry_point('crisprdisco', 'console_scripts', 'disco')()
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 722, in call
return self.main(args, kwargs)
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 535, in invoke
return callback(args, **kwargs)
File "/opt/app/crisprdisco/cli/script.py", line 85, in disco
casSearch(query_locations, subject_locations, date, evalue, idcutoff, lengthcutoff, working_outdir=workingdir, final_outdir=outdir)
File "/opt/app/crisprdisco/casPROTidentification.py", line 209, in casSearch
prot_filter(query,today, ID_cutoff, coverage_cutoff, workingdir=working_outdir, dry_run=dry_run_setting, output_dir=working_outdir)
File "/opt/app/crisprdisco/casPROTidentification.py", line 144, in prot_filter
no_duplicates.to_csv(os.path.join(output_dir, output_file_str))
File "/opt/conda/lib/python2.7/site-packages/pandas/core/frame.py", line 1524, in to_csv
formatter.save()
File "/opt/conda/lib/python2.7/site-packages/pandas/io/formats/format.py", line 1637, in save
compression=self.compression)
File "/opt/conda/lib/python2.7/site-packages/pandas/io/common.py", line 387, in _get_handle
f = open(path_or_buf, mode)
IOError: [Errno 13] Permission denied: u'test/temp_test_output/cas12b_blast_results_Seqs_TEST.csv'
test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_006449.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_023011.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_023060.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12b_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas9_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csf4gr11_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13c_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8b_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csn2_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c9_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c8_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csx10gr5_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas4_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8e_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8a_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_csm6_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8f_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasY_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8c_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas12c_generated_2017-07-17.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cmr1gr7_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas8u_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c5_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas12a_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13b_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas1_updated_2017-11-07.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c4_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Burstein_2017_CasX_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Makarova_2015_cas10d_generated_2017-05-15.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_combined_sets_cas3_generated_2017-05-24.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_c2c10_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Command line argument error: Argument "out". File is not accessible:test/temp_test_output/Ref_set_from_Shmakov_2017_cas13a_generated_2017-05-19.fasta.VS.NC_015847.faa.blastp' Traceback (most recent call last): File "/opt/conda/bin/disco", line 9, inreal 0m3.043s user 0m0.108s sys 0m0.034s