graph2chr.py error in compose_ctg

[yanwei-bio]

Hello Likui,

I'm using the graph2chr.py to generate the final assembly of Hifi reads. All the required files were generated, including the ec.fa, overlap, sg_edges_list and chr_paths. However, there comes the error as below:

Traceback (most recent call last): File "graph2chr.py", line 457, in main(sys.argv) File "graph2chr.py", line 453, in main run(**vars(args)) File "graph2chr.py", line 420, in run p_edge_lines, p_ctg_seq_chunks, p_total_score, p_total_length = compose_ctg(seqs, edge_data, ctg_id, one_path_edges, True) File "graph2chr.py", line 320, in compose_ctg rid, s, t, aln_score, idt, e_seq = edge_data[(vv, ww)] KeyError: ('m64257e_211206_205428/126289547/ccs:E', 'm64257e_211206_205428/134810423/ccs:E')

I'd checked the reported reads in KeyError. Nothing special was found. Could you please help me to solve the final step in assembly?

[likui345]

Hello yanwei, There is no overlap between these two reads. This problem is caused by Purge-dups. You can rerun hifiasm with the parameter -l 0.

[yanwei-bio]

Hi Likui, Thank you for your suggestion. I'd added the parameter -l 0 and rerun hifiasm and following graph2chr.py. However, there still reported the similar error but different reads.

File "graph2chr.py", line 457, in main(sys.argv) File "graph2chr.py", line 453, in main run(**vars(args)) File "graph2chr.py", line 420, in run p_edge_lines, p_ctg_seq_chunks, p_total_score, p_total_length = compose_ctg(seqs, edge_data, ctg_id, one_path_edges, True) File "graph2chr.py", line 320, in compose_ctg rid, s, t, aln_score, idt, e_seq = edge_data[(vv, ww)] KeyError: ('m64257e_211206_205428/64684781/ccs:B', 'm64257e_211206_205428/28445004/ccs:B')

Is there any code should be modified in this program?

[likui345]

Hi yanwei: You can check the file asm.ovlp.paf to see if there is any overlap between m64257e_211206_205428/64684781/ccs and m64257e_211206_205428/28445004/ccs. In the last step,you need to use the unfiltered overlap file(asm.ovlp.paf).

------------------ 原始邮件 ------------------ 发件人: "likui345/PGA" @.>; 发送时间: 2022年1月12日(星期三) 上午9:01 @.>; 抄送: "KUI @.**@.>; 主题: Re: [likui345/PGA] graph2chr.py error in compose_ctg (Issue #2)

Hi Likui, Thank you for your suggestion. I'd added the parameter -l 0 and rerun hifiasm and following graph2chr.py. However, there still reported the similar error but different reads.

File "graph2chr.py", line 457, in main(sys.argv) File "graph2chr.py", line 453, in main run(**vars(args)) File "graph2chr.py", line 420, in run p_edge_lines, p_ctg_seq_chunks, p_total_score, p_total_length = compose_ctg(seqs, edge_data, ctg_id, one_path_edges, True) File "graph2chr.py", line 320, in compose_ctg rid, s, t, aln_score, idt, e_seq = edge_data[(vv, ww)] KeyError: ('m64257e_211206_205428/64684781/ccs:B', 'm64257e_211206_205428/28445004/ccs:B')

Is there any code should be modified in this program?

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[Johnsonzcode]

@yanwei-bio, I met the same error. Maybe we can overlap HiFi reads by minimap2 and reformat the paf file. I am trying to do it.

[shimiao123]

@likui345 @yanwei-bio @Johnsonzcode ,I met the same error. My error information: Traceback (most recent call last): File "graph2chr.py", line 457, in main(sys.argv) File "graph2chr.py", line 453, in main run(**vars(args)) File "graph2chr.py", line 420, in run p_edge_lines, p_ctg_seq_chunks, p_total_score, p_total_length = compose_ctg(seqs, edge_data, ctg_id, one_path_edges, True) File "graph2chr.py", line 320, in compose_ctg rid, s, t, aln_score, idt, e_seq = edge_data[(vv, ww)] KeyError: ('m64438e_221116_021511/81789594/ccs:B', 'm64438e_221116_021511/102827493/ccs:E')

Everyone has solved this problem?

[Johnsonzcode]

You need to rerun HiFiasm with -l 0.