Add a few additional failures to our notes doc

scripts/variantstore/beta_docs/gvs-troubleshooting.md

@@ -5,22 +5,48 @@ Generally, if you have started the GVS workflow and it failed after ingestion, o
 ## Access and auth errors
 1. `Failed to create dataset: Access Denied: User does not have bigquery.datasets.create permission.`
    1. See steps 5 and 6 in the [quickstart](./gvs-quickstart.md) to assign the right permissions on your google project for your Terra proxy user.
-2. `BadRequestException: 400 Bucket is a requester pays bucket but no user project provided.`
+1. `BadRequestException: 400 Bucket is a requester pays bucket but no user project provided.`
    1. GVS can ingest data from a requester pays bucket by setting the optional `billing_project_id` input variable. This variable takes a string of a Google project ID to charge for the egress of the GVCFs and index files.
+1. `BigQuery error in mk operation: Not found: Dataset <project>:<dataset>`
+   Make sure there is a dataset in BQ and set up the proper permissions
 
 ## Runtime errors
-1. My workflow failed during ingestion, can I restart it?
-   1. If it fails during ingestion, yes, the GvsBeta workflow is restartable and will pick up where it left off.
-2. Duplicate sample names error: `ERROR: The input file ~{sample_names_file} contains the following duplicate entries:`
-   1. The GVS requires that sample names are unique because the sample names are used to name the samples in the VCF, and VCF format requires unique sample names. 
-   2. After deleting or renaming the duplicate sample, you can restart the workflow without any clean up.
-3. `BulkIngestGenomes/GvsBulkIngestGenomes/hash/call-ImportGenomes/GvsImportGenomes/hash/call-GetUningestedSampleIds/gvs_ids.csv Required file output '/cromwell_root/gvs_ids.csv' does not exist.`
+### Ingestion-Specific Issues
+These are issues that occur almost immediately --- often because of mis-named headers or incorrect paths
+Note that if your workflow failed during ingestion, generally, the GvsBeta workflow is restartable and will pick up where it left off.
+
+1. GVS is running very slowly!
+   1. Confirm your GVCFs are reblocked. If your GVS workflow is running very slowly compared to the example runtimes in the workspace, you may have run GVS on GVCFs that have not been reblocked. 
+1.  `Duplicate sample names error: ERROR: The input file ~{sample_names_file} contains the following duplicate entries:`
+   1. The GVS requires that sample names are unique because the sample names are used to name the samples in the VCF, and VCF format requires unique sample names.
+   1. After deleting or renaming the duplicate sample, you can restart the workflow without any clean up.
+1. During Ingest: `Required file output '/cromwell_root/gvs_ids.csv' does not exist.`
    1. If you've attempted to run GVS more than once in the same BigQuery dataset, you may see this error. Please delete the dataset and create a new one. We recommend naming the new dataset something different than the one you deleted.
-4. AssignIds failure with error message: `BigQuery error in mk operation: Not found: Dataset`
-   1. This is saying that GVS was unable to find the BigQuery dataset specified in the inputs. If you haven't created a BigQuery dataset prior to running the workflow, you can follow the steps in [the quickstart](./gvs-quickstart.md). If you created it and still see this error, check the naming of the dataset matches your input specified and that the google project in the inputs is correct. Lastly, confirm you have set up the correct permissions for your Terra proxy account following the instructions in the quickstart. 
-
-## Reblocking
-1. `htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: file:///cromwell_root/v1_[uuid]`
-   1. If you are running ReblockGVCF from a TDR snapshot, you will see this error if you did not check the “Convert DRS URLs to Google Cloud Storage Paths (gs://)" box before exporting the snapshot.
-2. GVS is running very slowly!
-   1. If your GVS workflow is running very slowly compared to the example runtimes in the workspace, you may have run GVS on GVCFs that have not been reblocked. Confirm your GVCFs are reblocked.
+1. AssignIds failure with error message: `BigQuery error in mk operation: Not found: Dataset`
+   1. This is saying that GVS was unable to find the BigQuery dataset specified in the inputs. If you haven't created a BigQuery dataset prior to running the workflow, you can follow the steps in the quickstart. If you created it and still see this error, check the naming of the dataset matches your input specified and that the google project in the inputs is correct. Lastly, confirm you have set up the correct permissions for your Terra proxy account following the instructions in the quickstart.
+1. Ingest failure with error message: `raise ValueError("vcf column not in table")`
+   1. if you have given an incorrect name for the vcf column or the vcf index column
+   1. You can simply restart the workflow with the correct names
+1. Ingest failure with error message: `Invalid resource name projects/{your_project_id}; Project id: {your_project_id}.`
+   1. This occurs if you have given the incorrect name of the project.
+   1. Restart the workflow with the correct name
+1. Ingest failure with `Max id is 0. Exiting.`
+   1. Please fully delete the GVS BigQuery dataset and recreate it as you did originally. Then kick off the ingest just as you did before--Make sure call caching is turned off.
+1. Ingest failure: There is already a list of sample names. This may need manual cleanup. Exiting.
+   1. Clean up the BQ dataset manually by deleting it and recreating it fresh
+   1. Make sure to keep the call caching off and run it again
+1. Ingest failure with error message: `A USER ERROR has occurred: Cannot be missing required value for <a required annotation>`
+   1. (e.g. alternate_bases.AS_RAW_MQ, RAW_MQandDP or RAW_MQ)
+   1. This means that there is at least one incorrectly formatted sample in your data model. Confirm your GVCFs are reblocked. If the incorrectly formatted samples are a small portion of your callset and you wish to just ignore them, simply delete the from the data model and restart the workflow without them. There should be no issue with starting from here as none of these samples were loaded.
+   1. Please see the full list of [required information in a GVCF to work in GVS](./run-your-own-samples.md#gvcf-annotations)
+1. Ingest failure with: `Lock table error`
+   1. This error usually occurs when a previous error has been fixed but perhaps not completely and it is best to start with a clean slate.
+   1. The lock table can be found inside your GVS BigQuery dataset  -- `{your_dataset_id}.sample_id_assignment_lock`. 
+   1. It is created to prevent duplicate sample errors and if you see this, it's better to start fresh. 
+   1. Please fully delete the GVS BigQuery dataset and recreate it as you did originally. Then kick off the ingest just as you did before--Make sure call caching is turned off.
+
+
+
+
+
+