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Godotcoffee / AlignGraph2

Similar genome assisted reassembly pipeline for PacBio long reads
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No config #2

Open zsdxgl opened 2 years ago

zsdxgl commented 2 years ago

Dear Godotcoffee,

Traceback (most recent call last): File "AlignGraph2/AlignGraph2.py", line 389, in script.split_helper.split_pre_process(ctg_path, ref_path, ctg_to_ref_path, input_dir, sp_input_dir) File "/AlignGraph2/script/split_helper.py", line 21, in split_pre_process with open(cfg_path, 'r') as cf: FileNotFoundError: [Errno 2] No such file or directory: '/working_dir/input/p/config.txt'

An error ocurred. Any suggestion?

Godotcoffee commented 2 years ago

Sorry for taking so long to reply. Because this project is now mainly maintained there, I didn't see this issue immediately. According to the description, the problem may be caused by the module "pre_process" (runs in the AlignGraph2.py, line 369, the executable file located in "AlignGraph2/PAGraph/build/pre_process"). The "pre_process" must ensure that there is output to "working_dir/input/p/config.txt". But now I don't know the exact problem, you can try print the command details of line 369 and manually run at the command line to see what happens.