about haphic reassign

[mikeqiu00]

老师，您好！
在 haphic reassign 中,出现了错误
错误内容如下：
2025-01-08 11:31:58 <HapHiC_reassign.py> [run] Program started, HapHiC version: 1.0.6 (update: 2024.09.10)
2025-01-08 11:31:58 <HapHiC_reassign.py> [run] Python version: 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0]
2025-01-08 11:31:58 <HapHiC_reassign.py> [run] Command: /sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py p_ctg.fa full_links.pkl mcl_inflation_1.9.clusters.txt paired_links.clm --nclusters 21 --threads 48
2025-01-08 11:31:58 <HapHiC_cluster.py> [parse_fasta] Parsing input FASTA file...
2025-01-08 11:33:32 <HapHiC_reassign.py> [parse_pickle] Parsing input pickle file...
2025-01-08 11:33:32 <HapHiC_reassign.py> [parse_clusters] Parsing .clusters.txt file...
Traceback (most recent call last):
File "/sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py", line 920, in
main()
File "/sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py", line 916, in main
run(args, 'HapHiC_reassign.log')
File "/sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py", line 839, in run
ctg_group_dict, group_RE_dict = parse_clusters(args.clusters, RE_site_dict, fa_dict, args.min_group_len)
File "/sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py", line 152, in parse_clusters
if min_group_len and sum([fa_dict[ctg][1] for ctg in cols[2:]]) / 1000000 < min_group_len:
File "/sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py", line 152, in
if min_group_len and sum([fa_dict[ctg][1] for ctg in cols[2:]]) / 1000000 < min_group_len:
KeyError: 'ptg000116l:50888501-97238460'
Traceback (most recent call last):
File "/sofeware/biosofeware/HapHiC/haphic", line 117, in
subprocess.run(commands, check=True)
File "/cluster/home/miniconda3/envs/haphic/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/sofeware/biosofeware/HapHiC/scripts/HapHiC_reassign.py', 'p_ctg.fa', 'full_links.pkl', 'mcl_inflation_1.9.clusters.txt', 'paired_links.clm', '--nclusters', '21', '--threads', '48']' returned non-zero exit status 1
在 clustering 中 HapHiC_cluster.log 文件中 The "best" inflation:
2025-01-08 04:27:48 <HapHiC_cluster.py> [recommend_inflation] You could try inflation from 1.9 (length ratio = 0.75)
不知道这是什么原因?
谢谢曾老师！希望您方便时解答一下，我将不胜感激！

[zengxiaofei]

Hi @mikeqiu00,

KeyError: 'ptg000116l:50888501-97238460'

If you have enabled the --correct_nrounds parameter, the contigs may be split into multiple fragments in the first step. You should use the corrected contigs (corrected_asm.fa) generated in this process instead of your raw p_ctg.fa file when performing reassignment, as noted in our documentation.

Note: If assembly correction has been performed, use corrected_asm.fa as input FASTA file instead of asm.fa.

Best regards,
Xiaofei

[mikeqiu00]

老师，您好！
感谢您的回复，我确实使用错了输入的 .fa 文件。
再次感谢老师