Skip to content

Commit 74f9855

Browse files
shenwei356shenwei356
committed
update benchmark results
1 parent fee9e82 commit 74f9855

File tree

4 files changed

+40
-38
lines changed

4 files changed

+40
-38
lines changed

‎README.md‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -43,12 +43,12 @@ Running at this scale has previously only been achieved by [Phylign](https://git
4343

4444
**With LexicMap** (48 CPUs),
4545

46-
|Query |Genome hits|Time |RAM |
47-
|:-------------------|----------:|-----:|------:|
48-
|A 1.3-kb marker gene|37,164 |52s |4.1 GB |
49-
|A 1.5-kb 16S rRNA |1,949,496 |13m53s|13.1 GB|
50-
|A 52.8-kb plasmid |544,619 |23m30s|17.5 GB|
51-
|1003 AMR genes |25,702,419 |4h02m |41.3 GB|
46+
|Query |Genome hits|Time |RAM |
47+
|:-------------------|----------:|---------:|------:|
48+
|A 1.3-kb marker gene|37,164 |36 s |4.1 GB |
49+
|A 1.5-kb 16S rRNA |1,949,496 |10 m 41 s |14.1 GB|
50+
|A 52.8-kb plasmid |544,619 |19 m 20 s |19.3 GB|
51+
|1003 AMR genes |25,702,419 |187 m 40 s|55.4 GB|
5252

5353

5454
More documents: https://bioinf.shenwei.me/LexicMap.

‎docs/content/_index.md‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -66,12 +66,12 @@ Step 2: searching
6666

6767
Using LexicMap to search in the whole **2,340,672** Genbank+Refseq prokaryotic genomes with 48 CPUs.
6868

69-
|Query |Genome hits|Time |RAM |
70-
|:-------------------|----------:|-----:|------:|
71-
|A 1.3-kb marker gene|37,164 |52s |4.1 GB |
72-
|A 1.5-kb 16S rRNA |1,949,496 |13m53s|13.1 GB|
73-
|A 52.8-kb plasmid |544,619 |23m30s|17.5 GB|
74-
|1003 AMR genes |25,702,419 |4h02m |41.3 GB|
69+
|Query |Genome hits|Time |RAM |
70+
|:-------------------|----------:|------:|-----:|
71+
|A 1.3-kb gene|37,164 |36s |4.1GB |
72+
|A 1.5-kb 16S rRNA |1,949,496 |10m41s |14.1GB|
73+
|A 52.8-kb plasmid |544,619 |19m20s |19.3GB|
74+
|1003 AMR genes |25,702,419 |187m40s|55.4GB|
7575

7676

7777
***Blastn** is unable to run with the same dataset on common servers as it requires >2000 GB RAM*.

‎docs/content/introduction/_index.md‎

Lines changed: 24 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -51,12 +51,12 @@ Running at this scale has previously only been achieved by [Phylign](https://git
5151

5252
**With LexicMap** (48 CPUs),
5353

54-
|Query |Genome hits|Time |RAM |
55-
|:-------------------|----------:|-----:|------:|
56-
|A 1.3-kb marker gene|37,164 |52s |4.1 GB |
57-
|A 1.5-kb 16S rRNA |1,949,496 |13m53s|13.1 GB|
58-
|A 52.8-kb plasmid |544,619 |23m30s|17.5 GB|
59-
|1003 AMR genes |25,702,419 |4h02m |41.3 GB|
54+
|Query |Genome hits|Time |RAM |
55+
|:-------------------|----------:|---------:|------:|
56+
|A 1.3-kb marker gene|37,164 |36 s |4.1 GB |
57+
|A 1.5-kb 16S rRNA |1,949,496 |10 m 41 s |14.1 GB|
58+
|A 52.8-kb plasmid |544,619 |19 m 20 s |19.3 GB|
59+
|1003 AMR genes |25,702,419 |187 m 40 s|55.4 GB|
6060

6161

6262
## Quick start
@@ -198,46 +198,48 @@ Phylign only has the index for AllTheBacteria HQ dataset.
198198

199199
GTDB complete (402,538 genomes):
200200

201-
202201
|query |query_len |tool |genome_hits|genome_hits(qcov>50)|time |RAM |
203-
|:--------------|:------------|:--------------|----------:|-------------------:|---------:|-------:|
204-
|a marker gene |1,299 bp |LexicMap |5,170 |5,143 |3.0 s |1.4 GB |
202+
|:--------------|------------:|:--------------|----------:|-------------------:|---------:|-------:|
203+
|a marker gene |1,299 bp |LexicMap |5,170 |5,143 |17 s |1.4 GB |
205204
| | |Blastn |7,121 |6,177 |2,171 s |351.2 GB|
206-
|a 16S rRNA gene|1,542 bp |LexicMap |303,925 |278,141 |92 s |4.9 GB |
205+
|a 16S rRNA gene|1,542 bp |LexicMap |303,925 |278,141 |235 s |4.4 GB |
207206
| | |Blastn |301,197 |277,042 |2,353 s |378.4 GB|
208-
|a plasmid |52,830 bp |LexicMap |63,108 |1,190 |87 s |4.8 GB |
207+
|a plasmid |52,830 bp |LexicMap |63,108 |1,190 |499 s |4.6 GB |
209208
| | |Blastn |69,311 |2,308 |2,262 s |364.7 GB|
210-
|1033 AMR genes |1 kb (median)|LexicMap |3,867,003 |2,228,339 |1,254 s |21.4 GB |
209+
|1033 AMR genes |1 kb (median)|LexicMap |3,867,003 |2,228,339 |4,350 s |16.3 GB |
211210
| | |Blastn |5,357,772 |2,240,766 |4,686 s |442.1 GB|
212211

213212

213+
214214
AllTheBacteria HQ (1,858,610 genomes):
215215

216216

217217
|query |query_len |tool |genome_hits|genome_hits(qcov>50)|time |RAM |
218-
|:--------------|:------------|:--------------|----------:|-------------------:|---------:|-------:|
219-
|a marker gene |1,299 bp |LexicMap |27,963 |27,953 |41.7 s |3.4 GB |
218+
|:--------------|------------:|:--------------|----------:|-------------------:|---------:|-------:|
219+
|a marker gene |1,299 bp |LexicMap |27,963 |27,953 |31 s |3.4 GB |
220220
| | |Phylign_local |7,936 | |30 m 48 s |77.6 GB |
221221
| | |Phylign_cluster|7,936 | |28 m 33 s | |
222-
|a 16S rRNA gene|1,542 bp |LexicMap |1,857,761 |1,740,000 |13 m 24 s |13.7 GB |
222+
|a 16S rRNA gene|1,542 bp |LexicMap |1,857,761 |1,740,000 |9 m 36 s |14.9 GB |
223223
| | |Phylign_local |1,017,765 | |130 m 33 s|77.0 GB |
224224
| | |Phylign_cluster|1,017,765 | |86 m 41 s | |
225-
|a plasmid |52,830 bp |LexicMap |468,821 |3,618 |20 m 48 s |15.9 GB |
225+
|a plasmid |52,830 bp |LexicMap |468,821 |3,618 |15 m 55 s |15.7 GB |
226226
| | |Phylign_local |46,822 | |47 m 33 s |82.6 GB |
227227
| | |Phylign_cluster|46,822 | |39 m 34 s | |
228-
|1033 AMR genes |1 kb (median)|LexicMap |21,288,000 |12,148,642 |168 m 48 s|49.2 GB |
228+
|1033 AMR genes |1 kb (median)|LexicMap |21,288,000 |12,148,642 |138 m 55 s|49.9 GB |
229229
| | |Phylign_local |1,135,215 | |156 m 08 s|85.9 GB |
230230
| | |Phylign_cluster|1,135,215 | |133 m 49 s| |
231231

232232

233+
233234
Genbank+RefSeq (2,340,672 genomes):
234235

235236
|query |query_len |tool |genome_hits|genome_hits(qcov>50)|time |RAM |
236-
|:--------------|:------------|:--------------|----------:|-------------------:|---------:|-------:|
237-
|a marker gene |1,299 bp |LexicMap |37,164 |37,082 |51.9 s |4.1 GB |
238-
|a 16S rRNA gene|1,542 bp |LexicMap |1,949,496 |1,381,974 |13 m 53 s |13.1 GB |
239-
|a plasmid |52,830 bp |LexicMap |544,619 |6,563 |23 m 30 s |17.5 GB |
240-
|1033 AMR genes |1 kb (median)|LexicMap |25,702,419 |14,692,624 |242 m 25 s|56.2 GB |
237+
|:--------------|------------:|:--------------|----------:|-------------------:|---------:|-------:|
238+
|a marker gene |1,299 bp |LexicMap |37,164 |37,082 |36 s |4.1 GB |
239+
|a 16S rRNA gene|1,542 bp |LexicMap |1,949,496 |1,381,974 |10 m 41 s |14.1 GB |
240+
|a plasmid |52,830 bp |LexicMap |544,619 |6,563 |19 m 20 s |19.3 GB |
241+
|1033 AMR genes |1 kb (median)|LexicMap |25,702,419 |14,692,624 |187 m 40 s|55.4 GB |
242+
241243

242244
Notes:
243245
- All files are stored on a server with HDD disks. No files are cached in memory.

‎docs/content/[email protected]‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
Query Genome hits Time RAM
2-
A 1.3-kb marker gene 37,164 52s 4.1 GB
3-
A 1.5-kb 16S rRNA 1,949,496 13m53s 13.1 GB
4-
A 52.8-kb plasmid 544,619 23m30s 17.5 GB
5-
1003 AMR genes 25,702,419 4h02m 41.3 GB
2+
A 1.3-kb marker gene 37,164 36 s 4.1 GB
3+
A 1.5-kb 16S rRNA 1,949,496 10 m 41 s 14.1 GB
4+
A 52.8-kb plasmid 544,619 19 m 20 s 19.3 GB
5+
1003 AMR genes 25,702,419 187 m 40 s 55.4 GB

0 commit comments

Comments
 (0)