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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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ERROR: No sequences read for genome XXX. Check recipe for correctness ( Hal ) #47

Closed shameem356 closed 4 years ago

shameem356 commented 5 years ago

Hello @fenderglass ,

I am getting the below error message while running Ragout with HAL option. Even the solution #18 (removed block size 5000 removed from ragout/shared/config.py) also didnt work.Here is my ragout.log and rcp file . Please can you suggest me how to solve this issue

Error Message :

[19:17:01] root: INFO: "datePalm" synteny blocks coverage: 0.3427% [19:17:01] root: INFO: "coconut" synteny blocks coverage: 0.1424% [19:17:01] root: INFO: "rice" synteny blocks coverage: 0.001001% [19:17:01] root: INFO: "sorghum" synteny blocks coverage: 0.0005158% [19:17:01] root: INFO: "oil" synteny blocks coverage: 0.04902% [19:17:01] root: WARNING: Some genomes have low synteny block coverage - results can be inaccurate. Possible reasons:

  1. Genome is too distant from others
  2. Synteny block parameters are chosen incorrectly Try to change synteny blocks paramsters or remove this genome from the comparison [19:17:01] root: DEBUG: Read 1242 reference sequences [19:17:01] root: DEBUG: Read 446 target sequences [19:17:01] root: DEBUG: 377 target sequences left after indel filtering [19:17:02] root: DEBUG: 372 target sequences left after repeat filtering [19:17:02] root: DEBUG: Branch lengths: [91.0625, 91.0625, 85.875, 66.125, 1e-06, 199.625, 1e-06, 266.66666666666663], mu = 0.0116448326055 [19:17:02] root: INFO: Inferred tree: ('coconut' : 91.0625, ('datePalm' : 85.875, ('rice' : 1e-06, ('sorghum' : 1e-06, 'oil' : 266.666666667) : 199.625) : 66.125) : 91.0625) [19:17:02] root: INFO: Processing permutation files [19:17:02] root: INFO: Reading Ragout_synteny_corection/output/hal-workdir/500/blocks_coords.txt [19:17:02] root: ERROR: An error occured while running Ragout: [19:17:02] root: ERROR: No sequences read for genome sorghum. Check recipe for correctness.
mikolmogorov commented 5 years ago

Looks like the reference genomes are too distant from the target, and that is why some references simply do not have any synteny blocks.

  1. Could you give more details on the target and reference genomes? What is the approximate nucleotide similarity between them? Are they complete or fragmented (looks like at least some of them are fragmented)?

  2. Did you use the HAL version that I suggested in the previous discussion (not the newest one)? maf2synteny has generated a warning that alignment blocks are overlapping, which in general is not expected..

I would also try to leave only one reference that is closest to the target and try again. You don't need to recompute HAL alignment for this, just remove all but one references from the recipe.