Exception: Two haplotypes are not equal length

[liukeweiaway]

File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/paraphase.py", line 146, in process_gene phaser_call = phaser.call()._asdict() File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/genes/rccx_phaser.py", line 438, in call ) = self.phase_haps(raw_read_haps) File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/phaser.py", line 1242, in phase_haps ass_haps, original_haps, hcn = hap_graph.run(debug=debug, make_plot=debug) File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/haplotype_assembler.py", line 1149, in run final_haps = self.filter_low_support_haps(final_haps, min_count=4, debug=debug) File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/haplotype_assembler.py", line 182, in filter_low_support_haps read_support = self.match_reads_and_haplotypes(reads, haps_to_assess) File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/haplotype_assembler.py", line 679, in match_reads_and_haplotypes match, mismatch, extend = VariantGraph.compare_two_haps( File "/lustre/home/acct-medfzx/medfzx-lkw/miniconda3_x86/envs/paraphase/lib/python3.10/site-packages/paraphase/haplotype_assembler.py", line 652, in compare_two_haps raise Exception("Two haplotypes are not equal length") Exception: Two haplotypes are not equal length

[liukeweiaway]

I tried printing the values of hap1 and hap2 during program execution and observed that they are 54:53. I'm unsure about the reason for this occurrence.

[xiao-chen-xc]

Hi @liukeweiaway, would it be possible to extract a small bam file (chr6:31980000-32046800, hg38) and share with me? You could either upload it here or email it to me (xchen@pacificbiosciences.com). Thanks.