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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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No overlaps found #104

Closed Yukicathy closed 5 years ago

Yukicathy commented 5 years ago

Hi ， I'm trying to assemble a 4M genome using ONT reads (100x),but Flye seems to have problems with overlap; [2019-04-26 13:56:18] DEBUG: Running with k-mer size: 15 [2019-04-26 13:56:18] DEBUG: Running with minimum overlap 5000 [2019-04-26 13:56:18] DEBUG: Metagenome mode: N [2019-04-26 13:56:18] INFO: Reading sequences [2019-04-26 13:56:39] DEBUG: Building positional index [2019-04-26 13:56:40] DEBUG: Total sequence: 886141702 bp [2019-04-26 13:56:40] DEBUG: Expected read coverage: 221535425 [2019-04-26 13:56:40] INFO: Generating solid k-mer index [2019-04-26 13:56:40] DEBUG: Hard threshold set to 5 [2019-04-26 13:56:40] DEBUG: Started k-mer counting [2019-04-26 13:56:58] INFO: Counting k-mers (1/2): [2019-04-26 13:57:48] INFO: Counting k-mers (2/2): [2019-04-26 13:59:48] DEBUG: Estimated minimum kmer coverage: 11465 [2019-04-26 13:59:48] DEBUG: Filtered 35297327 erroneous k-mers [2019-04-26 13:59:48] DEBUG: Repetitive k-mer frequency: 6717740 [2019-04-26 13:59:48] DEBUG: Filtered 0 repetitive k-mers (0) [2019-04-26 13:59:48] INFO: Filling index table [2019-04-26 13:59:49] DEBUG: Sampling rate: 1 [2019-04-26 13:59:49] DEBUG: Solid k-mers: 4 [2019-04-26 13:59:49] DEBUG: K-mer index size: 335887 [2019-04-26 13:59:49] DEBUG: Mean k-mer frequency: 83971.8 [2019-04-26 14:02:39] DEBUG: Sorting k-mer index [2019-04-26 14:02:39] DEBUG: Peak RAM usage: 2 Gb [2019-04-26 14:02:39] INFO: Extending reads [2019-04-26 14:02:39] DEBUG: Estimating overlap coverage [2019-04-26 15:30:57] WARNING: No overlaps found! [2019-04-26 15:30:57] INFO: Overlap-based coverage: 0 [2019-04-26 15:30:57] INFO: Median overlap divergence: 0

Do I need to modify the Minimum overlap length？

mikolmogorov commented 5 years ago

Hi,

Could you send the full log file and provide some details about the dataset?

Yukicathy commented 5 years ago

flye.log Thank you very much

mikolmogorov commented 5 years ago

Your expected genome is 4Mb, but your --genome-size is set to 50. You need to input 4m instead.

mikolmogorov commented 5 years ago

Note the difference between 4 and 4m - the second translates to 4000000 basepairs.