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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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assembly error No disjointigs were assembled #704

Closed isabelluo closed 1 month ago

isabelluo commented 1 month ago

Hi I was running flye on Geneious and the following are the log files generated ERROR: No disjointigs were assembled - please check if the read type and genome size parameters are correct

Failed to run: /Users/luoyizhen/Library/Application Support/Geneious/plugins/Flye/resources/MacOS/bin/flye --nano-raw input_0_Unpaired.fastq --threads 8 --genome-size 5m --iterations 1 -t 10 --out-dir out, exit code: 1

Flye reported the following errors: [2024-05-21 12:42:00] INFO: Starting Flye 2.9.1-b1780 [2024-05-21 12:42:00] INFO: >>>STAGE: configure [2024-05-21 12:42:00] INFO: Configuring run [2024-05-21 12:42:02] INFO: Total read length: 196211018 [2024-05-21 12:42:02] INFO: Input genome size: 5000000 [2024-05-21 12:42:02] INFO: Estimated coverage: 39 [2024-05-21 12:42:02] INFO: Reads N50/N90: 10205 / 2801 [2024-05-21 12:42:02] INFO: Minimum overlap set to 3000 [2024-05-21 12:42:02] INFO: >>>STAGE: assembly [2024-05-21 12:42:02] INFO: Assembling disjointigs [2024-05-21 12:42:02] INFO: Reading sequences [2024-05-21 12:42:09] INFO: Counting k-mers: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-05-21 12:45:23] INFO: Filling index table (1/2) 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-05-21 12:47:55] INFO: Filling index table (2/2) 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-05-21 12:58:34] INFO: Extending reads [2024-05-21 13:20:29] INFO: Overlap-based coverage: 3466 [2024-05-21 13:20:29] INFO: Median overlap divergence: 0.0566537 0% 100% [2024-05-21 14:33:46] INFO: Assembled 0 disjointigs [2024-05-21 14:33:46] INFO: Generating sequence [2024-05-21 14:33:46] INFO: Filtering contained disjointigs [2024-05-21 14:33:46] INFO: Contained seqs: 0 [2024-05-21 14:33:47] ERROR: No disjointigs were assembled - please check if the read type and genome size parameters are correct [2024-05-21 14:33:47] ERROR: Pipeline aborted

What could the problem be?

mikolmogorov commented 1 month ago

Duplicate of https://github.com/fenderglass/Flye/issues/128. Please check this thread and see if anything applies. If not, feel free to continue in the original thread.