mikolmogorov
commented
10 months ago Could you please submit hapdup.log and log files from flye_* directories inside the hapdup output dir?
Closed santoshe1 closed 6 months ago
mikolmogorov
commented
10 months ago Could you please submit hapdup.log and log files from flye_* directories inside the hapdup output dir?
Hello Team,
Thank you for this wonderful tool. I am processing a GIAB dataset - HG002 and would like to report a bug/error during the run of HapDup with Flye throwing an error to not create polished_1.fasta. Please see the error log below:
[](Nov 14, 2023 09:17:51:hapdup.fasta_parser.FastaError: [Errno 2] No such file or directory: '/obs/research_ont/test/hapdup/HG002/1/task-2-hapdup/hapdup/HG002/flye_hap_1/polished_1.fasta' Nov 14, 2023 09:17:51: raise FastaError(e) Nov 14, 2023 09:17:51: File "/usr/local/lib/python3.8/dist-packages/hapdup/fasta_parser.py", line 74, in stream_sequence Nov 14, 2023 09:17:51: for hdr, seq in stream_sequence(filename): Nov 14, 2023 09:17:51: File "/usr/local/lib/python3.8/dist-packages/hapdup/fasta_parser.py", line 37, in read_sequence_dict Nov 14, 2023 09:17:51: fasta_dict = fp.read_sequence_dict(input_fasta) Nov 14, 2023 09:17:51: File "/usr/local/lib/python3.8/dist-packages/hapdup/apply_inversions.py", line 23, in apply_inversions Nov 14, 2023 09:17:51: apply_inversions(inversions_hp, polished_flye_hap[hp], final_dual_asm[hp], hp) Nov 14, 2023 09:17:51: File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 266, in main Nov 14, 2023 09:17:51: sys.exit(main()) Nov 14, 2023 09:17:51: File "/usr/local/bin/hapdup", line 8, in
Nov 14, 2023 09:17:51:Traceback (most recent call last):
Nov 14, 2023 09:17:51:
Nov 14, 2023 09:17:51:During handling of the above exception, another exception occurred:)
Could you please help me resolve this issue?
Thank you