Testing Release v1.0.0-rc.1

[sorelfitzgibbon]

Tested on PCAWG-63 realigned BAMs.

• F2: 1.5 GB assigned to each process, retry adds 2 GB
• CollectWgsMetrics failed on the very large BAM, but succeeded on retry (3.5 GB).
• Within metapipeline these would be run on an F72 with 4 GB starting allocated memory.

Bam	Bam size	algorithm	allocated mem	status	duration	%cpu	peak_rss
DO15110-tumor	231.5 GB	samtools-stats	1.5 GB	completed	3h 25m 2s	79.8	5 MB
DO15110-tumor	231.5 GB	CollectWgsMetrics	1.5 GB	FAILED	2h 28m 24s
DO15110-tumor	231.5 GB	CollectWgsMetrics	3.5 GB	RETRY: completed	6h 30m 14s	91.4%	1.5 GB
DO15110-normal	88 GB	samtools-stats	1.5 GB	completed	1h 21m 48s	84	5.4 MB
DO15110-normal	88 GB	CollectWgsMetrics	1.5 GB	completed	3h 40m 23s	95.7	960 MB
DO218695-tumor	151.5 GB	samtools-stats	1.5 GB	completed	2h 38m 3s	73.3	5.1 MB
DO218695-tumor	151.5 GB	CollectWgsMetrics	1.5 GB	completed	4h 54m 52s	90	1.1 GB
DO218695-normal	175 GB	samtools-stats	1.5 GB	completed	5h 13m 58s	43	5.7 MB
DO218695-normal	175 GB	CollectWgsMetrics	1.5 GB	FAILED	4h 21m 54s
DO218695-normal	175 GB	CollectWgsMetrics	3.5 GB	RETRY:completed	8h 8m 47s	67	1.2 GB

Full trace files:
/hot/user/sfitzgibbon/PCAWG-63/sqc-bam-output/generate-SQC-BAM-1.0.0-rc.1/DO15110/log-generate-SQC-BAM-1.0.0-rc.1-20240312T045704Z/nextflow-log/trace.txt
/hot/user/sfitzgibbon/PCAWG-63/sqc-bam-output/generate-SQC-BAM-1.0.0-rc.1/DO218695/log-generate-SQC-BAM-1.0.0-rc.1-20240312T050135Z/nextflow-log/trace.txt