diff --git a/docs/source/_static/css/glow.css b/docs/source/_static/css/glow.css new file mode 100644 index 000000000..912d88b2b --- /dev/null +++ b/docs/source/_static/css/glow.css @@ -0,0 +1,3 @@ +ul.simple li p:last-of-type { + margin-bottom: 0px; +} diff --git a/docs/source/conf.py b/docs/source/conf.py index f1b6b3cc6..4827ea958 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -107,6 +107,8 @@ # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +html_css_files = ['css/glow.css'] + html_logo = '../../static/glow_logo_horiz_color_dark_bg.png' html_favicon = '../../static/favicon.ico' diff --git a/docs/source/index.rst b/docs/source/index.rst index 1303c961f..43b868546 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -12,6 +12,7 @@ machine learning, enabling the scale of the cloud for genomics workflows. getting-started etl/index tertiary/index + troubleshooting additional-resources .. modules diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst new file mode 100644 index 000000000..6b970afd2 --- /dev/null +++ b/docs/source/troubleshooting.rst @@ -0,0 +1,20 @@ +Troubleshooting +=============== + +- Job is slow or OOMs (throws an ``OutOfMemoryError``) while using an aggregate like ``collect_list`` or + ``sample_call_summary_stats`` + + * Try disabling the `ObjectHashAggregate + `_ by setting + ``spark.sql.execution.useObjectHashAggregateExec`` to ``false`` + +- Job is slow or OOMs while writing to partitioned table + + * This error can occur when reading from highly compressed files. Try decreasing + ``spark.files.maxPartitionBytes`` to a smaller value like ``33554432`` (32MB) + +- My VCF looks weird after merging VCFs and saving with ``bigvcf`` + + * When saving to a VCF, the samples in the genotypes array must be in the same order for each row. + This ordering is not guaranteed when using ``collect_list`` to join multiple VCFs. Try sorting + the array using ``sort_array``.