search

DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
184 stars 44 forks source link

Empty dataset #102

Closed demolnau closed 3 years ago

demolnau commented 4 years ago

I have an assembly from Spades that for some reason will not create a dataset with blobtools2. I tried out my code with an organism that was already assembled and on ncbi and didn't have any trouble. So you have any idea why this genome from a Spades assembly won't play nice? I am throwing a little bit of of the fasta sequence below to show the format.

NODE_1_length_3471173_cov_2.719110 AAGTTAAATTAAAAATTTATTTAAAAAAAAAAAAAATAATAATAATAATAATAATAATAA TTACAAGTACAGGATAATATAAGAATAAGATATTGAAATTGATTGGATATTTTATGCAAG TTTTAATAGCAGTGACTCGATAATTATTTTACAATATTATGTCTGTAATTTGATAAAAAT GATGGAATAAAAAATTATTAAGAAAAAATTTCTTCTCTTTTTAAATCTCTACCTTCAATG ATATTACTTGTTAAATATTTGGTTATAGTATCGATTGAATATCAAGTCAGAACACGTAGC GGGATAATATATCCACGAGGATTACCAAACAATGTACAGCAATTTCAAAACATTCCAATA ACATCAATAAAAAAATAGTTCAACACCGTAGTAAAAATTATAGCGATCCCACTTCAATCT ...

Code: /home/demolnau/work/blobtoolkit/blobtools2/blobtools create \ --fasta /home/demolnau/work/pego_contaminants/pego_scaffolds_30X.fa \ --meta /home/demolnau/work/pego_contaminants/pego_scaffolds_30X.yaml \ --taxdump /home/demolnau/work/blobtoolkit/taxdump \ /home/demolnau/work/pego_contaminants/datasets/pegoscapus_spades_assembly_30X

Please send help!

DRL commented 3 years ago

Hi demolnau,

different blobtools, you want to ask here: https://github.com/blobtoolkit/blobtools2/issues

cheers,

dom