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tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV
MIT License
250 stars 36 forks source link

empty pickle for self mapping #138

Closed baozg closed 7 months ago

baozg commented 9 months ago

Hi, @tjiangHIT

If I used cuteSV to validate the genome assembly error (HiFi reads mapping back to the assembly itself). Some pickles will be empty, but cuteSV will report errors to these regions although the output looks fine.

Traceback (most recent call last):
  File "/ebio/abt6_projects7/conda/env/bin/cuteSV", line 1267, in <module>
    run(sys.argv[1:])
  File "/ebio/abt6_projects7/conda/env/bin/cuteSV", line 1263, in run
    main_ctrl(args, argv)
  File "/ebio/abt6_projects7/conda/env/bin/cuteSV", line 1230, in main_ctrl
    with open("%sresults/%s.pickle"%(temporary_dir,chrom), "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: './LACR-C-4_tmp/results/Chr5.pickle'
Meltpinkg commented 8 months ago

Hello, @baozg

Sorry for my late reply. This has been fixed in the newest version. Please git clone cuteSV via GitHub and install it. Hope it will help.

Best, Shuqi