Dependancy Error on CADD installation

[sreeshmaraj]

I am trying to install the CADD tool v1.6. i downloaded the Zip file from GitHub and installed snakemake, when i runned the install.sh in a new conda environment and am getting some conflict error. I am attaching the error file here. v.16_error.txt

I also tried to install version 1.5 and am getting some conflict error and also attaching the error message here.

v1.5_error.txt

I wanted to execute CADD and any help will be appreciable.

Thank you in advance.

[aerval]

Hi,

Yes, that unfortunately happens because conda is unfortunately not stable as maintainers keep deleting and changing prior versions of different packages. This creates dependencies issues every few weeks. I do not have the resources to update this right now but you can replace in the file Snakefile all instances of envs/environment.yaml by envs/environment_minimal.yaml and try to resolve/install with that one. (we replace that one at some point since it stopped resolving for some users but its entirely possible that it resolves now). Hopefully this helps,

[sreeshmaraj]

Thank you for your response but I am getting some other errors now.

`./CADD.sh -o cadd_standalone -a test/input.vcf --CADD version 1.6 CADD-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved. Running snakemake pipeline: snakemake /tmp/tmp.ma69PK56dy/input.tsv.gz --use-conda --conda-prefix /home/sreeshma/CADD/CADD-scripts-master/envs --cores 1 --configfile /home/sreeshma/CADD/CADD-scripts-master/config/config_GRCh38_v1.6.yml --snakefile /home/sreeshma/CADD/CADD-scripts-master/Snakefile -q Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count

---

annotation 1 imputation 1 join 1 prepare 1 prescore 1 score 1 total 6

Select jobs to execute... Activating conda environment: envs/592bdf516157604235519e81ddd225c7 Select jobs to execute... Activating conda environment: envs/592bdf516157604235519e81ddd225c7 Removing temporary output /tmp/tmp.ma69PK56dy/input.prepared.vcf. Select jobs to execute... Activating conda environment: envs/592bdf516157604235519e81ddd225c7 Possible precedence issue with control flow operator at /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

-------------------- EXCEPTION -------------------- MSG: ERROR: No cache found for homo_sapiens, version 95

STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:328 STACK Bio::EnsEMBL::VEP::CacheDir::init /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227 STACK Bio::EnsEMBL::VEP::CacheDir::new /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7_/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_fromcache /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::getall /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91 STACK Bio::EnsEMBL::VEP::BaseRunner::get_allAnnotationSources /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175 STACK Bio::EnsEMBL::VEP::Runner::init /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/Runner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::run /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/share/ensembl-vep-95.1-0/modules/Bio/EnsEMBL/VEP/Runner.pm:194 STACK toplevel /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7_/bin/vep:225 Date (localtime) = Thu Dec 21 11:14:24 2023 Ensembl API version = 95

Traceback (most recent call last): File "/home/sreeshma/CADD/CADD-scripts-master/src/scripts/annotateVEPvcf.py", line 33, in vcfreader = vcf.Reader(sys.stdin) File "/home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/lib/python2.7/site-packages/vcf/parser.py", line 300, in init self._parsemetainfo() File "/home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7/lib/python2.7/site-packages/vcf/parser.py", line 317, in _parsemetainfo line = next(self.reader) StopIteration [Thu Dec 21 11:14:24 2023] Error in rule annotation: jobid: 5 input: /tmp/tmp.ma69PK56dy/input.novel.vcf output: /tmp/tmp.ma69PK56dy/input.anno.tsv.gz conda-env: /home/sreeshma/CADD/CADD-scripts-master/envs/592bdf516157604235519e81ddd225c7 shell:

    cat /tmp/tmp.ma69PK56dy/input.novel.vcf         | vep --quiet --cache --offline --dir $CADD/data/annotations/GRCh38_v1.6/vep             --buffer 1000 --no_stats --species homo_sapiens             --db_version=95 --assembly GRCh38             --format vcf --regulatory --sift b --polyphen b --per_gene --ccds --domains             --numbers --canonical --total_length --vcf --force_overwrite --output_file STDOUT         | python $CADD/src/scripts/annotateVEPvcf.py             -c $CADD/config/references_GRCh38_v1.6.cfg         | gzip -c > /tmp/tmp.ma69PK56dy/input.anno.tsv.gz

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job annotation since they might be corrupted: /tmp/tmp.ma69PK56dy/input.anno.tsv.gz Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-12-21T111422.611069.snakemake.log`

I wanted to ask you, is it required to have the vep cache files there in the annotation folder?

Thank you, Sreeshma Raj K