Open Audra-Leigh opened 1 year ago
Hi @Audra-Leigh,
Thank you for your issue post.
Apologies for the confusion. For the run
pipeline, if you used:
yapim run -i /path/to/genome_dir -p $EukMS_run -o out -c run-pipeline.yaml
then, for the report
pipeline, you would use:
yapim run -p $EukMS_report -o out -c report-pipeline.yaml
Notice that, in the second command, the -i
flag is not provided - the report
pipeline will only annotate the input data that was processed by the run
pipeline. Also, the output directories are the same in both cases - the data is shared between the pipeline runs.
Hopefully this helps, please let me know if there are any further issues.
Chris
Good afternoon,
I'm trying to run your pipeline by utilizing commands for EukMS_run and EukMS_report. I keep getting an error message pertaining to busco. In the .yaml file, I have all the information for the system and the libraries. Maybe I'm entering the wrong information in the yaml file for report processing.
For busco I have the following information: Quality:
Number of threads task will use
threads: 10
Amount of memory task will use (in GB)
memory: 16 time: 4:00:00 skip: false dependencies: Busco: program: busco mode: prot lineage: eukaryota FLAGS: -f
Here is the code for the job submission:
yapim run -i /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/eukmeta/21FACS/results/run/21FACS-1000/ -c /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/eukmeta/jobs/21FACS-report-config.yaml -p /users/PAS1212/osu10462/EukMetaSanity/bin/report-pipeline/ -o /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/eukmeta/21FACS/report/
I've tried variations of prot and protein (I tried this due to busco github page). I get the following error message:
Traceback (most recent call last): File "/users/PAS1212/osu10462/miniconda3/envs/EukMS_report/lib/python3.8/site-packages/yapim/tasks/task.py", line 303, in try_run self.run() File "/users/PAS1212/osu10462/EukMetaSanity/bin/report-pipeline/dependencies/busco/busco.py", line 30, in run "-i", self.input["prot"], KeyError: 'prot'
How do I fix this? Am I missing some key piece of information?
Thanks
Audra-Leigh