Open ChristopherRichie opened 3 months ago
Hi, Run again without this parameter --db_directory //data/chrisr/wf-clone-validation-db
- if you do want to supply the database you first need to download it but the same database is now included in the workflow by default.
my script worked after i removed that vestigal parameter.... thanks.
I am getting "good" results with version 1.3.1. can you direct me to where the "default database" is located?
the "INPUTS" table indicates that "db_directory" is a tar.gz, but I am unable to locate it in the github folders. I would like to see how the default db is organized.
thanks
A copy of it is here, internally it is part of the package files for plannotate. https://github.com/mmcguffi/pLannotate/releases/download/v1.2.0/BLAST_dbs.tar.gz
Operating System
Windows 10
Other Linux
centos Rocky Linux 8.7 (Green Obsidian)
Workflow Version
v1.2.0
Workflow Execution
EPI2ME Desktop application
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-clone-validation -r v1.2.0 \ -c //data/chrisr/nextflow.config.Qi \ -profile biowulflocal \ --basecaller_cfg $basecaller_config \ --fastq "./"$output"/"$bc'_sorted_wf-basecalling.fq.gz' \ --out_dir $clone_validation_output \ --db_directory //data/chrisr/wf-clone-validation-db \ --threads 14
Workflow Execution - CLI Execution Profile
None
What happened?
|||||||||| _ __ _ __ ____ |||||||||| | ____| _ | | \/ | __| | | | | ||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | ||||| | |_| /| | / /| | | | |_|| | (| | |) _ \ |||||||||| |____|_| |_|___|| ||| ||\,|._/|/ |||||||||| wf-clone-validation v1.2.0-g2c04b9d
Core Nextflow options revision : v1.2.0 runName : intergalactic_hodgkin containerEngine: singularity launchDir : /gpfs/gsfs12/users/chrisr/CAM0237/no_sample/20240607_1721_MC-110461_APQ435_7b46463a workDir : /gpfs/gsfs12/users/chrisr/CAM0237/no_sample/20240607_1721_MC-110461_APQ435_7b46463a/work projectDir : /home/chrisr/.nextflow/23.04.1/assets/epi2me-labs/wf-clone-validation userName : chrisr profile : biowulflocal configFiles : /home/chrisr/.nextflow/23.04.1/assets/epi2me-labs/wf-clone-validation/nextflow.config, /data/chrisr/nextflow.config.Qi
Input Options fastq : ./BC06_basecalling/BC06_sorted_wf-basecalling.fq.gz
Output Options out_dir : BC06_clone_validation
Advanced Options db_directory : //data/chrisr/wf-clone-validation-db
Miscellaneous Options threads : 14
!! Only displaying parameters that differ from the pipeline defaults !!
If you use epi2me-labs/wf-clone-validation for your analysis please cite:
This is epi2me-labs/wf-clone-validation v1.2.0-g2c04b9d.
WARN: Nextflow version 23.04.1 does not match workflow required version: >=23.04.2 -- Execution will continue, but things may break! Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. executor > local (2) executor > local (2) executor > local (2) executor > local (16) [cd/21dd09] process > fastcat (1) [100%] 1 of 1 ✔ [a7/3e7a8b] process > pipeline:checkIfEnoughReads (1) [100%] 1 of 1 ✔ [df/b587e1] process > pipeline:assembleCore (1) [100%] 1 of 1 ✔ [4f/dd33e7] process > pipeline:lookup_medaka_model (1) [100%] 1 of 1 ✔ [ad/1f278b] process > pipeline:medakaPolishAssembly (1) [100%] 1 of 1 ✔ [63/763b83] process > pipeline:downsampledStats (1) [100%] 1 of 1 ✔ [f0/166092] process > pipeline:findPrimers (1) [100%] 1 of 1 ✔ [64/e4ce4e] process > pipeline:medakaVersion [100%] 1 of 1 ✔ [62/ebfedb] process > pipeline:flyeVersion [100%] 1 of 1 ✔ [82/ec3703] process > pipeline:getVersions [100%] 1 of 1 ✔ [cc/792f5b] process > pipeline:getParams [100%] 1 of 1 ✔ [9e/ebb9c0] process > pipeline:inserts [100%] 1 of 1 ✔ [60/675690] process > pipeline:assembly_qc (1) [100%] 1 of 1 ✔ [5c/ce8e45] process > pipeline:runPlannotate (1) [ 0%] 0 of 1 [b6/b87e3b] process > pipeline:assemblyMafs (1) [100%] 1 of 1 ✔ [- ] process > pipeline:report - [92/700a3d] process > output (1) [100%] 1 of 1 ERROR ~ Error executing process > 'pipeline:runPlannotate (1)'
Caused by: Process
pipeline:runPlannotate (1)
terminated with an error exit status (1)Command executed:
if [ -e "assemblies/OPTIONAL_FILE" ]; then assemblies="" else assemblies="--sequences assemblies/" fi workflow-glue run_plannotate $assemblies --database wf-clone-validation-db
Command exit status: 1
Command output: (empty)
Command error: /home/epi2melabs/conda/lib/python3.8/site-packages/plannotate/annotate.py:218: DeprecationWarning: invalid escape sequence | problem_name = "pdb|(.*)|" [13:38:23 - workflow_glue] Starting entrypoint. 2024-06-10 13:38:23.632 Warning: to view this Streamlit app on a browser, run it with the following command:
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information