Workflow error

[oliviatoles]

Hello I am receiving this error could you please help

WorkflowError: MissingInputException: Missing input files for rule markdown: output: /home/thie0149/toles008/IDF_project/allpilot/Output/Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.html wildcards: file=Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme affected files: Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.md MissingInputException: Missing input files for rule markdown: output: /home/thie0149/toles008/IDF_project/allpilot/Output/aberrant-splicing-pipeline_index.html wildcards: file=aberrant-splicing-pipeline_index affected files: aberrant-splicing-pipeline_index.md

[vyepez88]

Hi, please share more details. Is this in the demo dataset or your own? If it's your own, please try running the demo before. Which DROP version?

[oliviatoles]

Hello, it is for my own dataset. I have run the demo before successfully and I am using the most recent update of DROP.

Thank you

On Wed, May 10, 2023 at 5:02 PM Vicente Yepez @.***> wrote:

Hi, please share more details. Is this in the demo dataset or your own? If it's your own, please try running the demo before. Which DROP version?

— Reply to this email directly, view it on GitHub https://github.com/gagneurlab/drop/issues/462#issuecomment-1542369685, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2HQ7Q2P7XUBGR3SQQS66P3XFOUYZANCNFSM6AAAAAAX4SLVWQ . You are receiving this because you authored the thread.Message ID: @.***>

[vyepez88]

Hi, which command generated this error? Did the pipeline start and ended at some point or never started? Please be sure that all RNA IDs are properly spelled and all BAM files exist.

[oliviatoles]

This is what my error message says in its entirety WARNING: Using the mae defined genome instead of the globally defined one.

WARNING: 2 files missing in samples annotation. Ignoring... WARNING: Less than 30 IDs in DROP_GROUP outrider /home/thie0149/toles008/IDF_project/allpilot/Output/processed_data/aberrant_splicing/params/config/AberrantSplicing_config.tsv Param Files do not match. Updating to current Sample Annotation

check for missing R packages AberrantExpression has been turned off in the config file rnaVariantCalling has been turned off in the config file Structuring dependencies... Dependencies file generated at: /tmp/tmp031f5iz8

Building DAG of jobs... WorkflowError: MissingInputException: Missing input files for rule markdown: output: /home/thie0149/toles008/IDF_project/allpilot/Output/Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.html wildcards: file=Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme affected files: Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.md MissingInputException: Missing input files for rule markdown: output: /home/thie0149/toles008/IDF_project/allpilot/Output/aberrant-splicing-pipeline_index.html wildcards: file=aberrant-splicing-pipeline_index affected files: aberrant-splicing-pipeline_index.md

On Tue, May 16, 2023 at 9:15 AM Vicente Yepez @.***> wrote:

Hi, which command generated this error? Did the pipeline start and ended at some point or never started? Please be sure that all RNA IDs are properly spelled and all BAM files exist.

— Reply to this email directly, view it on GitHub https://github.com/gagneurlab/drop/issues/462#issuecomment-1549122790, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2HQ7Q2TIGKGX2BUC54FLDDXGMSSVANCNFSM6AAAAAAX4SLVWQ . You are receiving this because you authored the thread.Message ID: @.***>

[vyepez88]

Hi, can you please tell me which command generated this error? Also, be sure you're using the latest DROP. I see this as a potential mistake: WARNING: 2 files missing in samples annotation

[AtaJadidAhari]

Hi @oliviatoles, any updates on this issue? Did you manage to resolve it?

[vyepez88]

Hi, be sure you have your config file like this:

aberrantSplicing:
    run: true