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cjneely10 / EukMetaSanity

Structural and functional annotation of eukaryotic metagenome-assembled genomes
GNU General Public License v3.0
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Report error 'prot' #18

Open Audra-Leigh opened 1 year ago

Audra-Leigh commented 1 year ago

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

cjneely10 commented 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