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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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No disjointigs were assembled - please check if the read type and genome size parameters are correct #708

Closed lqhungpt closed 3 months ago

lqhungpt commented 3 months ago

Hi Admin, I tried to use Flye to assemble Nanopore raw reads with super-accurate base calling. The N50 length for my raw read was under 1kb. However, although I input the correct genome size of my virus, I have issues like the one below. Can you show me the main problem? I tried with SPAdes assembly with the same reads, it gave me a contig with around 15kb.

[2024-06-04 23:37:00] INFO: Starting Flye 2.9.4-b1799 [2024-06-04 23:37:00] INFO: >>>STAGE: configure [2024-06-04 23:37:00] INFO: Configuring run [2024-06-04 23:37:00] INFO: Total read length: 5573764 [2024-06-04 23:37:00] INFO: Input genome size: 15000 [2024-06-04 23:37:00] INFO: Estimated coverage: 371 [2024-06-04 23:37:00] INFO: Reads N50/N90: 563 / 261 [2024-06-04 23:37:00] INFO: Minimum overlap set to 1000 [2024-06-04 23:37:00] INFO: Using longest 50x reads for contig assembly [2024-06-04 23:37:00] INFO: >>>STAGE: assembly [2024-06-04 23:37:00] INFO: Assembling disjointigs [2024-06-04 23:37:00] INFO: Reading sequences [2024-06-04 23:37:00] INFO: Building minimizer index [2024-06-04 23:37:00] INFO: Pre-calculating index storage 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-06-04 23:37:00] INFO: Filling index 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-06-04 23:37:05] INFO: Extending reads [2024-06-04 23:37:07] INFO: Overlap-based coverage: 21 [2024-06-04 23:37:07] INFO: Median overlap divergence: 0.0506971 0% 100% [2024-06-04 23:37:09] INFO: Assembled 0 disjointigs [2024-06-04 23:37:09] INFO: Generating sequence [2024-06-04 23:37:09] INFO: Filtering contained disjointigs [2024-06-04 23:37:09] INFO: Contained seqs: 0 [2024-06-04 23:37:09] ERROR: No disjointigs were assembled - please check if the read type and genome size parameters are correct [2024-06-04 23:37:09] ERROR: Pipeline aborted

mikolmogorov commented 3 months ago

Duplicate of https://github.com/fenderglass/Flye/issues/128. Please see if anything from that thread applies. If it does not resolve your issue, please follow up in the original thread.