Added some issues to troubleshooting.md

docs/troubleshooting.md

@@ -18,3 +18,102 @@ You can fix the issue by ...
 Second: Before re-running panpipes, we recommend deleting any intermediate files that were created in the previous run which
 broke halfway through.  
 
+
+
+### Error in Plot 10x metric task in ingestion when not starting from CellRanger outputs
+**NoneType error**
+
+First: check the log files to see what went wrong.
+- In this case the pipeline failed at:
+
+```
+TypeError: argument of type 'NoneType' is not iterable \
+```
+- After checking the error, check which log file to inspect by checking the Job line:
+```
+Task = def pipeline_ingest.aggregate_tenx_metrics_multi(...): \
+Job  = [None -> logs/tenx_metrics_multi_aggregate.log] \
+```
+
+- Inspect the log file for this process in `logs/tenx_metrics_multi_aggregate.log`
+- Check which Python script the code failed to know which task failed by looking at. In this case, the error was in:
+
+  ```
+  File "../panpipes/panpipes/python_scripts/aggregate_cellranger_summary_metrics.py"
+  ```
+- This indicates that in the pipeline.yml some parameter involving `10x metric` was set wrong, and by going to the beginning of the pipeline.log file it is clear that the `plot_10X_metrics` was set to `True` although the data did not come from CellRanger, which means `plot_10X_metrics` should be set to `False` since the input data was an Andata object.
+- Thus, by changing the `pipeline.yml` `plot_10X_metrics` to `False` the issue is fixed
+- To rerun, first delete the `logs/tenx_metrics_multi_aggregate.log` file
+- Then run `panpipes ingest make full`
+
+
+
+### Error in Plot 10x metric task in ingestion when starting from CellRanger outputs using 10X.h5 format
+**KeyError**
+
+First: check the log files to see what went wrong.
+- In this case the pipeline failed at:
+
+```
+raise KeyError(key) from err \
+KeyError: 'Median UMI counts per cell' \
+```
+
+- After checking the error, check what was the last task run:
+
+```
+Traceback (most recent call last): \
+File "/data/leuven/344/vsc34406/Miniconda3/envs/Panpipes/lib/python3.9/site-packages/panpipes/python_scripts/aggregate_cellranger_summary_metrics.py", line 268, in <module> \
+```
+
+- In this case, the error was while running the Python script `aggregate_cellranger_summary_metrics.py`
+- This means that a particular string could not be found. In this case, it was the `Median UMI counts per cell`
+
+
+
+
+
+
+### Wrong cell_cycle gene list inputted
+**No valid genes were passed for scoring**
+
+First: check the log files to see what went wrong.
+- In this case the pipeline failed at:
+```
+ValueError: No valid genes were passed for scoring. \
+```
+
+ - After checking the error, check which log file to inspect by checking the Job line:
+```
+ Task = def pipeline_ingest.run_rna_qc(...): \
+ Job  = [None -> logs/run_scanpy_qc_rna.log, mouse_integrated_cell_metadata.tsv, mouse_integrated_unfilt.h5mu] \
+```
+- In this case, also check the WARNING:
+
+```
+  WARNING: genes are not in var_names and ignored: ['MCM5', 'PCNA', 'TYMS', 'FEN1', 'MCM2', 'MCM4', 'RRM1', 'UNG', 'GINS2', 'MCM6', 'CDCA7', 'DTL', 'PRIM1', 'UHRF1', 'MLF1IP', 'HELLS', 'RFC2', 'RPA2', 'NASP', 'RAD51AP1', 'GMNN', 'WDR76', 'SLBP', 'CCNE2', 'UBR7', 'POLD3', 'MSH2', 'ATAD2', 'RAD51', 'RRM2', 'CDC45', 'CDC6', 'EXO1', 'TIPIN', 'DSCC1', 'BLM', 'CASP8AP2', 'USP1', 'CLSPN', 'POLA1', 'CHAF1B', 'BRIP1', 'E2F8'] \
+```
+- This shows that the gene list provided is not matching with the input data since **none** of the genes can be found. For example, this gene list is for humans only and the input data was from a mouse model which requires a mouse-specific gene list
+- To fix the issue simply change the preprocess pipeline.yml `custom_genes_file` to a mouse gene list provided in the `panpipes/resources`
+- Delete the log folders and any temp files
+- Run `panpipes ingest make ful`
+
+
+### Running preprocessed with RNA-only PlotQC error 
+**No such file or directory**
+First: check the log files to see what went wrong.
+- In this case the pipeline failed at:
+```
+FileNotFoundError: [Errno 2] No such file or directory:
+```
+ - After checking the error, check which log file to inspect by checking the Job line:
+```
+ Task = def pipeline_preprocess.filter_mudata(...): \
+ Job  = [None -> humanised_preprocessed.h5mu] \
+```
+- Before proceeding, double-check the `pipeline.yml` to see if the correct path was provided for the mudata object.
+- Once the user is sure the path is correct, the next step is to check the modalities in the `pipeline.yml`
+- In this case, the mudata object contains only RNA and that was the only modality set for `True`, however in the `plotqc` variable there are metrics for `prot_metrics` when there is no protein in the data.
+- To fix the issue, clear the metrics in `prot_metrics`
+- Delete the log folder and any temp files
+- Re-run `panpipes preprocess make full`