Analysis Pipeline Troubleshooting

Failure Type	Action
One or more pipeline steps fail	- Open the log file ./<AnalysisFolder>/Logs_Intermediates/pipeline_trace.txt. This log file displays each pipeline step run by the Nextflow workflow manager software. If a step fails, it is marked as FAILED. Each step generates log files that are stored in step-specific subfolders in the Logs_Intermediates folder. Review the log files in the relevant Logs_Intermediates folder for the step to identify potential sources of error. - Open the errors folder ./<AnalysisFolder>/errors. The workflow creates an error file, error_<NameOfFailedStep>.json, for each step that failed during analysis. For steps that fail per sample, there is a separately labeled file for each sample that failed each step error_<NameOfFailedStep>_<SampleIDIfRelevant>.json. These files contain the command and stdout and stderr from the step.
One or more samples are missing results for one or more variant types	Open the combined metrics output results file ./<AnalysisFolder>/Results/<PairId>/MetricsOutput.tsv. If a sample fails an analysis step, the Pair ID that contains the sample shows the failure under FAILED_STEPS in the Analysis Status section, and COMPLETED_ALL_STEPS shows as False. If available, review the individual log files for the failed steps under ./<AnalysisFolder>/Logs_Intermediates to identify potential sources of error.
Single exon (single probe) genes are still reported in the CNV VCF file, but not the CNV TSV file	No action needed; software is working as expected. For v2.6.1 and below, CNV events for genes with low probe coverage are not emitted to the Copy Number Variants section of our CombinedVariantOutput.tsv. However, you can still find these events in the cnv.vcf.gz. Due to the low probe coverage, accurate CNV calling has not been validated and as such they are emitted as REF These events are no longer included in the VCF starting in v2.6.2.