python version conflict

[Stephen8554]

Hi! Following your guidance, I installed CRISPRCasFinder firstly. However, the process runs into some errors during cas genes detection after finishing CRISPR genes detection.

Request: Single Genome, Phase: Gene Finding Finding genes in sequence #1 (526169 bp)...done! Traceback (most recent call last): File "/opt/AcrFinder/acrfinder-master/dependencies/CRISPRCasFinder/bin/macsyfinder", line 37, in from macsypy.search_systems import search_systems File "/opt/AcrFinder/acrfinder-master/dependencies/CRISPRCasFinder/macsyfinder-1.0.5/macsypy/search_systems.py", line 1027 """ SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 685-686: truncated \uXXXX escape No Cas results Nb of Cas in this sequence = 0 Secondary folders/files (Prodigal, CasFinder, rawFASTA, CRISPRFinderProperties) have been created

All CRISPRs = 9 All Cas = 0

CRISPRCasFinder will call the macsyFinder to detect cas genes. MacsyFinder requires Python2.7 while your README.md says that Python3.4 or new version is required to run AcrFinder.

[linnabrown]

Thank you for using our tool. In your sever you need both install python 2.7 and python 3. But python3. should be your main python interpreter. We will clarify this point about this.

Also, we recommend you to use docker to install our tool. Just one step to build all requirements

docker pull [OPTIONS] haidyi/acrfinder:latest

or you can install it by github

git clone https://github.com/haidyi/acrfinder.git
cd acrfinder
docker build -t [tag name] .

[Stephen8554]

Thanks! I am installing AcrFinder with docker. There are some problems occurred.

[root@wanglab4 test]# docker pull haidyi/acrfinder:latest latest: Pulling from haidyi/acrfinder df7e5105b466: Extracting [===========> ] 833.9 MB/3.752 GB f068f206b7d8: Download complete 64322be39581: Download complete e8610d37ffa9: Download complete d20f93c749c5: Download complete d14e585437d2: Download complete 7454ee621e34: Download complete 341582a6ed28: Download complete cf16b54d0273: Download complete aa0c732f38e9: Download complete 949ea3fc7e52: Download complete cb58b97a95fd: Download complete b6c9d3505751: Download complete 52e45d550808: Already exists 3d1c7fcbd1dc: Already exists 4e1bf54cd3be: Already exists a818d3439bf9: Already exists aec622c79675: Already exists d31d50821393: Already exists 1e5f2a0719e4: Already exists 0355e5d64e93: Already exists c46965895385: Already exists 993e7910424c: Already exists 0c2ac6811355: Already exists 2d148493030a: Already exists 2ff496487397: Already exists 08bea033bc82: Already exists 66f69e14fa74: Already exists 4e8628b6d9ef: Already exists f3691f9df8a0: Already exists 836315858273: Already exists b3fac6e69f95: Already exists e360b68cdc9a: Already exists 85c2b42f5508: Already exists 5d71ec22151b: Already exists 8e0e33ba157d: Already exists Pulling repository haidyi/acrfinder Could not reach any registry endpoint

[linnabrown]

we will give you the feedback asap.

[linnabrown]

Hi Stephen8554 . We just docker pull the pkg in a new server, but there is no this kind of error like yours. Did you try this command twice? If so, you need you remove these existing images. For example.

docker rmi 52e45d550808 
docker rmi 836315858273
...

[Stephen8554]

Hi linnabrown! I have updated my server from CentOS 6 to CentOS 7. And I have pulled the package from Doker Hub successfully. However, another problem occurred. I could not enter the interactive mode when I start the acrfinder. `[chengzhi@localhost ~]$ docker run haidyi/acrfinder /bin/bash [chengzhi@localhost ~]$ docker container ls -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES b8532ad291f9 haidyi/acrfinder "/bin/bash" 6 minutes ago Exited (0) 6 minutes ago pensive_franklin [chengzhi@localhost ~]$ docker info Client: Debug Mode: false

Server: Containers: 1 Running: 0 Paused: 0 Stopped: 1 Images: 2 Server Version: 19.03.12 Storage Driver: overlay2 Backing Filesystem: xfs Supports d_type: true Native Overlay Diff: true Logging Driver: json-file Cgroup Driver: cgroupfs Plugins: Volume: local Network: bridge host ipvlan macvlan null overlay Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog Swarm: inactive Runtimes: runc Default Runtime: runc Init Binary: docker-init containerd version: 7ad184331fa3e55e52b890ea95e65ba581ae3429 runc version: dc9208a3303feef5b3839f4323d9beb36df0a9dd init version: fec3683 Security Options: seccomp Profile: default Kernel Version: 3.10.0-1127.13.1.el7.x86_64 Operating System: CentOS Linux 7 (Core) OSType: linux Architecture: x86_64 CPUs: 16 Total Memory: 15.44GiB Name: localhost.localdomain ID: QOFX:YU4S:2AWA:YQQQ:R6GE:NRH2:GQI7:7V3V:WR4W:5SZ7:RTZZ:5IZT Docker Root Dir: /home/docker Debug Mode: false Registry: https://index.docker.io/v1/ Labels: Experimental: false Insecure Registries: 127.0.0.0/8 Live Restore Enabled: false`

[Stephen8554]

Hi linnabrown! I have installed acrfinder successfully. I install Ubuntu 20.04.1 and pull the image from Docker Hub. Then copy the GCF_000210795.2 from the sample_organisms folder to my home folder. Finally, I run the following command and get the results successfully! docker run --rm -it -v ~/GCF_000210795.2:/app/acrfinder/GCF_000210795.2 haidyi/acrfinder:latest python3 acr_aca_cri_runner.py -n GCF_000210795.2/GCF_000210795.2_genomic.fna -f GCF_000210795.2/GCF_000210795.2_genomic.gff -a GCF_000210795.2/GCF_000210795.2_protein.faa -o GCF_000210795.2/output_dir -z B -c 2 -p true -g true

Thanks for your help and I will close this issue.

[linnabrown]

Perfect