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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Error when using gff file as input #59

Open TsumaR opened 3 years ago

TsumaR commented 3 years ago

Thank you for developing such a great tool. I have a fasta file and a gff file that I want to use as input for clinker. However, I got the following error.

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[11:27:29] WARNING - Could not find parent gene of NODE_84_length_13759_cov_460.151_phanotate_53_geneCall_cds. Using coding sequence coordinates instead.
[11:27:29] WARNING - Could not find parent gene of NODE_84_length_13759_cov_460.151_phanotate_54_geneCall_cds. Using coding sequence coordinates instead.
[11:27:29] WARNING - Could not find parent gene of NODE_84_length_13759_cov_460.151_phanotate_55_geneCall_cds. Using coding sequence coordinates instead.
[11:27:29] WARNING - Could not find parent gene of NODE_84_length_13759_cov_460.151_phanotate_56_geneCall_cds. Using coding sequence coordinates instead.
Traceback (most recent call last):
  File "/home/wagatsuma/miniconda3/envs/clinker/bin/clinker", line 10, in <module>
    sys.exit(main())
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/clinker/main.py", line 208, in main
    clinker(
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/clinker/main.py", line 71, in clinker
    clusters = parse_files(paths)
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/clinker/classes.py", line 200, in parse_files
    cluster = parse_gff(path)
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/clinker/classes.py", line 68, in parse_gff
    gff = gffutils.create_db(
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/gffutils/create.py", line 1292, in create_db
    c.create()
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/gffutils/create.py", line 507, in create
    self._populate_from_lines(self.iterator)
  File "/home/wagatsuma/miniconda3/envs/clinker/lib/python3.9/site-packages/gffutils/create.py", line 629, in _populate_from_lines
    raise ValueError("No lines parsed -- was an empty file provided?")
ValueError: No lines parsed -- was an empty file provided?

I would appreciate it if you could let me know if there is any solution. I have attached a part of the gff file used for input below.

##gff-version 3
NODE_33_length_7462_cov_1658.36 PhATE   gene    2       163     .       +       .       ID=NODE_33_length_7462_cov_1658.36_phanotate_1_geneCall
NODE_33_length_7462_cov_1658.36 PhATE   CDS     2       163     .       +       .       ID=NODE_33_length_7462_cov_1658.36_phanotate_1_geneCall_cds
NODE_33_length_7462_cov_1658.36 PhATE   gene    362     577     .       -       .       ID=NODE_33_length_7462_cov_1658.36_phanotate_2_geneCall
NODE_33_length_7462_cov_1658.36 PhATE   CDS     362     577     .       -       .       ID=NODE_33_length_7462_cov_1658.36_phanotate_2_geneCall_cds
NODE_33_length_7462_cov_1658.36 PhATE   gene    902     1042    .       -       .       ID=NODE_33_length_7462_cov_1658.36_phanotate_3_geneCall
NODE_33_length_7462_cov_1658.36 PhATE   CDS     902     1042    .       -       .       ID=NODE_33_length_7462_cov_1658.36_phanotate_3_geneCall_cds

Best,