CoRAL reconstruct: didnt work

[rajithadp]

I tried to execute the reconstruct mode by
coral reconstruct --lr-bam /data/C1.bam --cnv-seed /data/C1_CNV_SEEDS.bed --output-dir /data/C1 --cn-seg /data/C1/C1.cns --log-file C1

It runs and generates the infer_breakpoint_graph.log, with no other results after a few hours.

[suhas-r]

Can you share the log / are there any errors in your console? CoRAL generates breakpoint graphs for all discovered amplicons before performing cycle extraction, so I would expect that *graph.txt files should be outputted within /data/C1. Breakpoint graph generation can take multiple hours for particularly large BAM files (multiple 100s of GB), though, so it's possible that that process is still ongoing.

[rajithadp]

Hi Suhas,

My BAM file is about 197GB in size, and I'm using 100GB of memory is that not enough to handle this? That may be why it takes more time. This is what my infer_breakpoint_graph.log looks like.

2025-01-16 09:22:30,561:DEBUG [infer_breakpoint_graph.py:2667] Parsed 1 seed amplicon intervals. 2025-01-16 09:22:30,561:DEBUG [infer_breakpoint_graph.py:2669] Seed interval: ['chr7', 53174682, 55339668] 2025-01-16 09:22:30,656:INFO [infer_breakpoint_graph.py:2678] Opened LR bam files. 2025-01-16 09:22:31,202:DEBUG [infer_breakpoint_graph.py:140] Total num LR copy number segments:5548. 2025-01-16 09:22:31,203:DEBUG [infer_breakpoint_graph.py:182] Use 18 LR copy number segments. 2025-01-16 09:22:31,203:DEBUG [infer_breakpoint_graph.py:185] Total length of LR copy number segments: 10484977. 2025-01-16 09:22:31,203:DEBUG [infer_breakpoint_graph.py:188] Average LR copy number: -0.0657606. 2025-01-16 09:23:44,973:INFO [infer_breakpoint_graph.py:204] LR normal cov =39.2027347317977, nnc=411039772, total_int_len=10484977. 2025-01-16 09:23:45,186:DEBUG [infer_breakpoint_graph.py:211] Reset min_cluster_cutoff to 39. 2025-01-16 09:23:45,186:INFO [infer_breakpoint_graph.py:2681] Completed parsing CN segment files.

[suhas-r]

I would expect that your resources are sufficient, but that it may just take longer to generate breakpoint graph files. Do you see any *_graph.txt files in your output directory yet (/data/C1)? How long have you waited?