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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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Detecting chimeric adjacencies Error #72

Closed sajjadasaf closed 3 years ago

sajjadasaf commented 3 years ago

I run ragout but finished with following error.

[09:18:51] INFO: "punica" synteny blocks coverage: 75.03% [09:18:51] INFO: "P1" synteny blocks coverage: 86.48% [09:19:01] INFO: Reading contigs file [09:19:06] INFO: Detecting chimeric adjacencies Traceback (most recent call last): File "/home/sajjad/miniconda3/bin/ragout", line 33, in sys.exit(load_entry_point('ragout==2.3', 'console_scripts', 'ragout')()) File "/home/sajjad/miniconda3/lib/python3.7/site-packages/ragout/main.py", line 295, in main _run_ragout(args) File "/home/sajjad/miniconda3/lib/python3.7/site-packages/ragout/main.py", line 200, in _run_ragout chim_detect = ChimeraDetector(raw_bp_graphs, run_stages, target_sequences) File "/home/sajjad/miniconda3/lib/python3.7/site-packages/ragout/breakpoint_graph/chimera_detector.py", line 28, in init self._make_hierarchical_breaks() File "/home/sajjad/miniconda3/lib/python3.7/site-packages/ragout/breakpoint_graph/chimera_detector.py", line 64, in _make_hierarchical_breaks break_pos = self._optimal_break(seq_name, *adjusted_break) File "/home/sajjad/miniconda3/lib/python3.7/site-packages/ragout/breakpoint_graph/chimera_detector.py", line 72, in _optimal_break seq = self.target_seqs[seq_name] KeyError: 'scafold596'

Here i attached rcp and ragout.log files ragout.log P1 (copy)..txt

sajjadasaf commented 3 years ago

Please please check it.

mikolmogorov commented 3 years ago

Probably you have changed the fasta headers in your contigs file into the form genome.sequence to generate .maf with SibeliaZ. You now need to supply the fasta file with original headers (before renaming) to run Ragout. Make sure that the header that gives you the KeyError exception is in the target fasta file.

Sorry for the confusion - SibeliaZ workflow is still experimental.