Running run_flye with params:
{
"workspace_name": "jgoff:narrative_1706820512139",
"long_reads_library": "PFAS_118_6_filtlong.reads",
"long_reads_type": "pacbio-hifi",
"meta": 0,
"min_overlap": null,
"output_contigset_name": "PFAS_118_6_CLR_flye.contigs2"
}
Getting long reads (from reads library object).
35425 long reads found, 0 under 1000 bp
command: seqtk rename /kb/module/work/tmp/0a7c56f3-cd1c-4add-b2d4-0f0e5014e1f2.single.fastq short > /kb/module/work/tmp/renamed_0a7c56f3-cd1c-4add-b2d4-0f0e5014e1f2.single.fastq
command: /kb/module/Flye-2.9.2/bin/flye --pacbio-hifi /kb/module/work/tmp/renamed_0a7c56f3-cd1c-4add-b2d4-0f0e5014e1f2.single.fastq --out-dir /kb/module/work/tmp/flye_41dbb935-9e46-48c9-81e1-c00216ca5c5f
[2024-02-06 15:57:55] INFO: Starting Flye 2.9.2-b1786
[2024-02-06 15:57:55] INFO: >>>STAGE: configure
[2024-02-06 15:57:55] INFO: Configuring run
[2024-02-06 15:57:56] INFO: Total read length: 349752517
[2024-02-06 15:57:56] INFO: Reads N50/N90: 9900 / 6952
[2024-02-06 15:57:56] INFO: Minimum overlap set to 7000
[2024-02-06 15:57:56] INFO: >>>STAGE: assembly
[2024-02-06 15:57:56] INFO: Assembling disjointigs
[2024-02-06 15:57:56] INFO: Reading sequences
[2024-02-06 15:57:57] INFO: Building minimizer index
[2024-02-06 15:57:57] INFO: Pre-calculating index storage
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 15:58:17] INFO: Filling index
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 15:59:30] INFO: Extending reads
[2024-02-06 16:00:15] INFO: Overlap-based coverage: 48
[2024-02-06 16:00:15] INFO: Median overlap divergence: 0.000307409
0% 90% 100%
[2024-02-06 16:04:06] INFO: Assembled 1 disjointigs
[2024-02-06 16:04:07] INFO: Generating sequence
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 16:04:09] INFO: Filtering contained disjointigs
0% 100%
[2024-02-06 16:04:11] INFO: Contained seqs: 0
[2024-02-06 16:04:11] INFO: >>>STAGE: consensus
[2024-02-06 16:04:11] INFO: Running Minimap2
[2024-02-06 16:05:36] INFO: Computing consensus
[2024-02-06 16:10:06] INFO: Alignment error rate: 0.003571
[2024-02-06 16:10:06] INFO: >>>STAGE: repeat
[2024-02-06 16:10:06] INFO: Building and resolving repeat graph
[2024-02-06 16:10:06] INFO: Parsing disjointigs
[2024-02-06 16:10:06] INFO: Building repeat graph
0% 100%
[2024-02-06 16:10:08] INFO: Median overlap divergence: 0
[2024-02-06 16:10:08] INFO: Parsing reads
[2024-02-06 16:10:09] INFO: Aligning reads to the graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 16:11:59] INFO: Aligned read sequence: 310663489 / 312012720 (0.995676)
[2024-02-06 16:11:59] INFO: Median overlap divergence: 0
[2024-02-06 16:11:59] INFO: Mean edge coverage: 55
[2024-02-06 16:11:59] INFO: Simplifying the graph
[2024-02-06 16:12:00] INFO: >>>STAGE: contigger
[2024-02-06 16:12:00] INFO: Generating contigs
[2024-02-06 16:12:00] INFO: Reading sequences
[2024-02-06 16:12:01] INFO: Generated 1 contigs
[2024-02-06 16:12:01] INFO: Added 0 scaffold connections
[2024-02-06 16:12:01] INFO: >>>STAGE: polishing
[2024-02-06 16:12:01] INFO: Polishing genome (1/1)
[2024-02-06 16:12:01] INFO: Running minimap2
[2024-02-06 16:13:26] INFO: Separating alignment into bubbles
[2024-02-06 16:19:36] INFO: Alignment error rate: 0.001246
[2024-02-06 16:19:36] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2024-02-06 16:23:11] INFO: >>>STAGE: finalize
[2024-02-06 16:23:11] INFO: Assembly statistics:
Total length: 5555804
Fragments: 1
Fragments N50: 5555804
Largest frg: 5555804
Scaffolds: 0
Mean coverage: 62
[2024-02-06 16:23:11] INFO: Final assembly: /kb/module/work/tmp/flye_41dbb935-9e46-48c9-81e1-c00216ca5c5f/assembly.fasta
Generating and saving report
Starting conversion of FASTA to KBaseGenomeAnnotations.Assembly
Running QUAST
start packing result files