incoherentian
commented
1 year ago Hi Mostafa,
It is a pretty small section of the dragonflye log buried among kmc, trimming polishing etc. Is it possible you missed it?
The log of the initial flye execution starts with [dragonflye] Running: flye & the relevant lines are prepended with [flye],
e.g.
``` [dragonflye] Running: flye --nano-raw READS.fq.gz -g 4792047 -i 0 --threads 12 -o flye 2>&1 | sed 's/^/[flye] /' | tee -a dragonflye.log [flye] [2023-10-05 14:11:46] INFO: Starting Flye 2.9.2-b1786 [flye] [2023-10-05 14:11:46] INFO: >>>STAGE: configure [flye] [2023-10-05 14:11:46] INFO: Configuring run [flye] [2023-10-05 14:11:49] INFO: Total read length: 203898539 [flye] [2023-10-05 14:11:49] INFO: Input genome size: 4792047 [flye] [2023-10-05 14:11:49] INFO: Estimated coverage: 42 [flye] [2023-10-05 14:11:49] INFO: Reads N50/N90: 19281 / 5303 [flye] [2023-10-05 14:11:49] INFO: Minimum overlap set to 5000 [flye] [2023-10-05 14:11:49] INFO: >>>STAGE: assembly [flye] [2023-10-05 14:11:49] INFO: Assembling disjointigs [flye] [2023-10-05 14:11:49] INFO: Reading sequences [flye] [2023-10-05 14:11:57] INFO: Counting k-mers: [flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [flye] [2023-10-05 14:13:14] INFO: Filling index table (1/2) [flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [flye] [2023-10-05 14:13:25] INFO: Filling index table (2/2) [flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [flye] [2023-10-05 14:13:47] INFO: Extending reads [flye] [2023-10-05 14:14:53] INFO: Overlap-based coverage: 37 [flye] [2023-10-05 14:14:53] INFO: Median overlap divergence: 0.0587165 [flye] 0% 90% 100% [flye] [2023-10-05 14:15:19] INFO: Assembled 2 disjointigs [flye] [2023-10-05 14:15:19] INFO: Generating sequence [flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [flye] [2023-10-05 14:15:24] INFO: Filtering contained disjointigs [flye] 0% 50% 100% [flye] [2023-10-05 14:15:28] INFO: Contained seqs: 0 [flye] [2023-10-05 14:15:28] INFO: >>>STAGE: consensus [flye] [2023-10-05 14:15:28] INFO: Running Minimap2 [flye] [2023-10-05 14:15:50] INFO: Computing consensus [flye] [2023-10-05 14:16:40] INFO: Alignment error rate: 0.073354 [flye] [2023-10-05 14:16:54] INFO: >>>STAGE: repeat [flye] [2023-10-05 14:16:54] INFO: Building and resolving repeat graph [flye] [2023-10-05 14:16:54] INFO: Parsing disjointigs [flye] [2023-10-05 14:16:54] INFO: Building repeat graph [flye] 0% 50% 100% [flye] [2023-10-05 14:17:04] INFO: Median overlap divergence: 0.0403617 [flye] [2023-10-05 14:17:05] INFO: Parsing reads [flye] [2023-10-05 14:17:12] INFO: Aligning reads to the graph [flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [flye] [2023-10-05 14:17:30] INFO: Aligned read sequence: 184160513 / 185129557 (0.994766) [flye] [2023-10-05 14:17:30] INFO: Median overlap divergence: 0.0160677 [flye] [2023-10-05 14:17:30] INFO: Mean edge coverage: 37 [flye] [2023-10-05 14:17:30] INFO: Simplifying the graph [flye] [2023-10-05 14:17:30] INFO: >>>STAGE: contigger [flye] [2023-10-05 14:17:30] INFO: Generating contigs [flye] [2023-10-05 14:17:30] INFO: Reading sequences [flye] [2023-10-05 14:17:34] INFO: Generated 2 contigs [flye] [2023-10-05 14:17:34] INFO: Added 0 scaffold connections [flye] [2023-10-05 14:17:34] INFO: >>>STAGE: finalize [flye] [2023-10-05 14:17:34] INFO: Assembly statistics: [flye] [flye] Total length: 4936081 [flye] Fragments: 2 [flye] Fragments N50: 4683859 [flye] Largest frg: 4683859 [flye] Scaffolds: 0 [flye] Mean coverage: 36 [flye] [flye] [2023-10-05 14:17:34] INFO: Final assembly: /path/to/flye/assembly.fasta ```(Randomly picked a pretty bad coverage example, woops, but still works as an example of it looking like a flye log!)
Hopefully that's helpful! BR, Ian
MostafaYA
Hello, Thanks for this great work. It would be nice not to remove the
flyelog information as they are not included in the dragonflye log file. Best regards Mostafa