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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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No sequences read for genome #3

Closed michoug closed 8 years ago

michoug commented 9 years ago

Hi,

I got this error while running your software

[11:54:55] INFO: Cooking Ragout... [11:54:55] INFO: Synteny block scale set to 'small' [11:54:55] INFO: Running Sibelia with block size 5000 [12:02:40] INFO: Running Sibelia with block size 500 [12:10:39] INFO: Running Sibelia with block size 100 [12:18:45] INFO: Phylogeny is taken from the recipe [12:18:45] INFO: Running Ragout with the block size 5000 [12:18:45] ERROR: An error occured while running Ragout: [12:18:45] ERROR: No sequences read for genome E3. Check recipe for correctness.

The recipe was this

.tree = (((((((KNP:0.00041,K02:0.00090):0.00066,3016:0.00130):0.02636,larvae:0.03996):0.00644,E3:0.22284):0.00422,Y412:0.02828):0.01905,HPL:0.01763):0.00478,E681:0.00486,(SC2:0.00236,M1:0.00348):0.00253);

.references = larvae,3016,K02,KNP,E681,M1,SC2,Y412,HPL .target = E3

*.circular = true .blocks = small

larvae.fasta = Paenibacillus larvae subsp. larvae DSM 25430.fna 3016.fasta = Paenibacillus mucilaginosus 3016.fna K02.fasta = Paenibacillus mucilaginosus K02.fna KNP.fasta = Paenibacillus mucilaginosus KNP414.fna E681.fasta = Paenibacillus polymyxa E681.fna M1.fasta = Paenibacillus polymyxa M1.fna SC2.fasta = Paenibacillus polymyxa SC2.fna Y412.fasta = Paenibacillus sp. Y412MC10.fna HPL.fasta = Paenibacillus terrae HPL-003.fna E3.fasta = PIL02S_Annotations_chromosome.fasta

Any ideas ?

mikolmogorov commented 9 years ago

It might be that the problematic genome is too distant from others, so Sibelia fails to identify large enough synteny blocks. It would be helpful, if you could send me the "ragout.log" file from the working directory (contains only some general statistics) as well as "sibelia-workdir" directory (contain permutation of synteny blocks in your genomes), so I can tell exactly what the problem is.