Flye error for PacBio sequence

[ghazalaziz]

I have been working on the pacbio sequence and trying to run assembly using Flye. Can anyone help for the issue

2023-11-04 18:51:34] INFO: Starting Flye 2.9.1-b1780
[2023-11-04 18:51:34] INFO: >>>STAGE: configure
[2023-11-04 18:51:34] INFO: Configuring run
[2023-11-04 18:52:12] INFO: Total read length: 3068330753
[2023-11-04 18:52:12] INFO: Reads N50/N90: 8681 / 6769
[2023-11-04 18:52:12] INFO: Minimum overlap set to 7000
[2023-11-04 18:52:12] INFO: >>>STAGE: assembly
[2023-11-04 18:52:12] INFO: Assembling disjointigs
[2023-11-04 18:52:12] INFO: Reading sequences
[2023-11-04 18:52:39] INFO: Counting k-mers:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-11-04 18:54:45] INFO: Filling index table (1/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-11-04 18:56:19] INFO: Filling index table (2/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-11-04 18:59:16] INFO: Extending reads
[2023-11-04 19:16:29] INFO: Overlap-based coverage: 870
[2023-11-04 19:16:29] INFO: Median overlap divergence: 0.0464289
0% 100%
[2023-11-04 22:30:47] INFO: Assembled 0 disjointigs
[2023-11-04 22:30:48] INFO: Generating sequence
[2023-11-04 22:30:48] INFO: Filtering contained disjointigs
[2023-11-04 22:30:48] INFO: Contained seqs: 0
[2023-11-04 22:30:49] ERROR: No disjointigs were assembled - please check if the read type and genome size parameters are correct
[2023-11-04 22:30:49] ERROR: Pipeline aborted

[bgruening]

@ghazalaziz please do not ask this question on different channels.

You need to play around with the Fly settings. Fly is trowing the error No disjointigs were assembled. If you google it you will find for example mikolmogorov/Flye#128 which recommends --asm-coverage 50 ... maybe you can try that.

[ghazalaziz]

Thank you for reply. I have been looking for solution and couldn't find it....so have to repost.

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