Running run_flye with params:
{
"workspace_name": "jgoff:narrative_1707234081078",
"long_reads_library": "PFAS_118_8filtlong.reads",
"long_reads_type": "pacbio-hifi",
"meta": 0,
"min_overlap": null,
"output_contigset_name": "PFAS_118_8flye.contigs"
}
Getting long reads (from reads library object).
32458 long reads found, 0 under 1000 bp
command: seqtk rename /kb/module/work/tmp/da6a88d9-7657-4464-9581-3534bf2d4732.single.fastq short > /kb/module/work/tmp/renamed_da6a88d9-7657-4464-9581-3534bf2d4732.single.fastq
command: /kb/module/Flye-2.9.2/bin/flye --pacbio-hifi /kb/module/work/tmp/renamed_da6a88d9-7657-4464-9581-3534bf2d4732.single.fastq --out-dir /kb/module/work/tmp/flye_0e6fe3d1-1acd-452b-a957-1de9d8eb7394
[2024-02-06 15:56:47] INFO: Starting Flye 2.9.2-b1786
[2024-02-06 15:56:47] INFO: >>>STAGE: configure
[2024-02-06 15:56:47] INFO: Configuring run
[2024-02-06 15:56:48] INFO: Total read length: 500011146
[2024-02-06 15:56:48] INFO: Reads N50/N90: 15215 / 12736
[2024-02-06 15:56:48] INFO: Minimum overlap set to 10000
[2024-02-06 15:56:48] INFO: >>>STAGE: assembly
[2024-02-06 15:56:48] INFO: Assembling disjointigs
[2024-02-06 15:56:48] INFO: Reading sequences
[2024-02-06 15:56:50] INFO: Building minimizer index
[2024-02-06 15:56:50] INFO: Pre-calculating index storage
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 15:57:22] INFO: Filling index
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[2024-02-06 16:00:04] INFO: Extending reads
[2024-02-06 16:02:04] INFO: Overlap-based coverage: 83
[2024-02-06 16:02:04] INFO: Median overlap divergence: 0
0% 40% 80% 90% 100%
[2024-02-06 16:06:45] INFO: Assembled 7 disjointigs
[2024-02-06 16:06:45] INFO: Generating sequence
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[2024-02-06 16:06:50] INFO: Filtering contained disjointigs
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[2024-02-06 16:06:52] INFO: Contained seqs: 0
[2024-02-06 16:06:52] INFO: >>>STAGE: consensus
[2024-02-06 16:06:52] INFO: Running Minimap2
[2024-02-06 16:09:25] INFO: Computing consensus
[2024-02-06 16:15:44] INFO: Alignment error rate: 0.001444
[2024-02-06 16:15:44] INFO: >>>STAGE: repeat
[2024-02-06 16:15:44] INFO: Building and resolving repeat graph
[2024-02-06 16:15:44] INFO: Parsing disjointigs
[2024-02-06 16:15:44] INFO: Building repeat graph
0% 10% 20% 40% 50% 70% 80% 100%
[2024-02-06 16:15:48] INFO: Median overlap divergence: 4.71298e-05
[2024-02-06 16:15:48] INFO: Parsing reads
[2024-02-06 16:15:49] INFO: Aligning reads to the graph
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[2024-02-06 16:19:22] INFO: Aligned read sequence: 497049335 / 500011146 (0.994077)
[2024-02-06 16:19:22] INFO: Median overlap divergence: 0
[2024-02-06 16:19:22] INFO: Mean edge coverage: 87
[2024-02-06 16:19:22] INFO: Simplifying the graph
[2024-02-06 16:19:22] INFO: >>>STAGE: contigger
[2024-02-06 16:19:22] INFO: Generating contigs
[2024-02-06 16:19:22] INFO: Reading sequences
[2024-02-06 16:19:24] INFO: Generated 7 contigs
[2024-02-06 16:19:24] INFO: Added 0 scaffold connections
[2024-02-06 16:19:24] INFO: >>>STAGE: polishing
[2024-02-06 16:19:24] INFO: Polishing genome (1/1)
[2024-02-06 16:19:24] INFO: Running minimap2
[2024-02-06 16:21:44] INFO: Separating alignment into bubbles
[2024-02-06 16:30:05] INFO: Alignment error rate: 0.000546
[2024-02-06 16:30:05] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 16:33:34] INFO: >>>STAGE: finalize
[2024-02-06 16:33:34] INFO: Assembly statistics:
Total length: 5622450
Fragments: 7
Fragments N50: 2935917
Largest frg: 2935917
Scaffolds: 0
Mean coverage: 88
[2024-02-06 16:33:34] INFO: Final assembly: /kb/module/work/tmp/flye_0e6fe3d1-1acd-452b-a957-1de9d8eb7394/assembly.fasta
Generating and saving report
Starting conversion of FASTA to KBaseGenomeAnnotations.Assembly
Running QUAST
start packing result files