update benchmark results

shenwei356 · Aug 15, 2024 · 74f9855 · 74f9855
1 parent fee9e82
commit 74f9855
Show file tree

Hide file tree

Showing 4 changed files with 40 additions and 38 deletions.
diff --git a/README.md b/README.md
@@ -43,12 +43,12 @@ Running at this scale has previously only been achieved by [Phylign](https://git
 
     **With LexicMap** (48 CPUs),
 
-    |Query               |Genome hits|Time  |RAM    |
-    |:-------------------|----------:|-----:|------:|
-    |A 1.3-kb marker gene|37,164     |52s   |4.1 GB |
-    |A 1.5-kb 16S rRNA   |1,949,496  |13m53s|13.1 GB|
-    |A 52.8-kb plasmid   |544,619    |23m30s|17.5 GB|
-    |1003 AMR genes      |25,702,419 |4h02m |41.3 GB|
+    |Query               |Genome hits|Time      |RAM    |
+    |:-------------------|----------:|---------:|------:|
+    |A 1.3-kb marker gene|37,164     |36 s      |4.1 GB |
+    |A 1.5-kb 16S rRNA   |1,949,496  |10 m 41 s |14.1 GB|
+    |A 52.8-kb plasmid   |544,619    |19 m 20 s |19.3 GB|
+    |1003 AMR genes      |25,702,419 |187 m 40 s|55.4 GB|
 
 
 More documents: https://bioinf.shenwei.me/LexicMap.

diff --git a/docs/content/_index.md b/docs/content/_index.md
@@ -66,12 +66,12 @@ Step 2: searching
 
 Using LexicMap to search in the whole **2,340,672** Genbank+Refseq prokaryotic genomes with 48 CPUs.
 
-|Query               |Genome hits|Time  |RAM    |
-|:-------------------|----------:|-----:|------:|
-|A 1.3-kb marker gene|37,164     |52s   |4.1 GB |
-|A 1.5-kb 16S rRNA   |1,949,496  |13m53s|13.1 GB|
-|A 52.8-kb plasmid   |544,619    |23m30s|17.5 GB|
-|1003 AMR genes      |25,702,419 |4h02m |41.3 GB|
+|Query               |Genome hits|Time   |RAM   |
+|:-------------------|----------:|------:|-----:|
+|A 1.3-kb        gene|37,164     |36s    |4.1GB |
+|A 1.5-kb 16S rRNA   |1,949,496  |10m41s |14.1GB|
+|A 52.8-kb plasmid   |544,619    |19m20s |19.3GB|
+|1003 AMR genes      |25,702,419 |187m40s|55.4GB|
 
 
 ***Blastn** is unable to run with the same dataset on common servers as it requires >2000 GB RAM*.

diff --git a/docs/content/introduction/_index.md b/docs/content/introduction/_index.md
@@ -51,12 +51,12 @@ Running at this scale has previously only been achieved by [Phylign](https://git
 
     **With LexicMap** (48 CPUs),
 
-    |Query               |Genome hits|Time  |RAM    |
-    |:-------------------|----------:|-----:|------:|
-    |A 1.3-kb marker gene|37,164     |52s   |4.1 GB |
-    |A 1.5-kb 16S rRNA   |1,949,496  |13m53s|13.1 GB|
-    |A 52.8-kb plasmid   |544,619    |23m30s|17.5 GB|
-    |1003 AMR genes      |25,702,419 |4h02m |41.3 GB|
+    |Query               |Genome hits|Time      |RAM    |
+    |:-------------------|----------:|---------:|------:|
+    |A 1.3-kb marker gene|37,164     |36 s      |4.1 GB |
+    |A 1.5-kb 16S rRNA   |1,949,496  |10 m 41 s |14.1 GB|
+    |A 52.8-kb plasmid   |544,619    |19 m 20 s |19.3 GB|
+    |1003 AMR genes      |25,702,419 |187 m 40 s|55.4 GB|
 
 
 ## Quick start
@@ -198,46 +198,48 @@ Phylign only has the index for AllTheBacteria HQ dataset.
 
 GTDB complete (402,538 genomes):
 
-
 |query          |query_len    |tool           |genome_hits|genome_hits(qcov>50)|time      |RAM     |
-|:--------------|:------------|:--------------|----------:|-------------------:|---------:|-------:|
-|a marker gene  |1,299 bp     |LexicMap       |5,170      |5,143               |3.0 s     |1.4 GB  |
+|:--------------|------------:|:--------------|----------:|-------------------:|---------:|-------:|
+|a marker gene  |1,299 bp     |LexicMap       |5,170      |5,143               |17 s      |1.4 GB  |
 |               |             |Blastn         |7,121      |6,177               |2,171 s   |351.2 GB|
-|a 16S rRNA gene|1,542 bp     |LexicMap       |303,925    |278,141             |92 s      |4.9 GB  |
+|a 16S rRNA gene|1,542 bp     |LexicMap       |303,925    |278,141             |235 s     |4.4 GB  |
 |               |             |Blastn         |301,197    |277,042             |2,353 s   |378.4 GB|
-|a plasmid      |52,830 bp    |LexicMap       |63,108     |1,190               |87 s      |4.8 GB  |
+|a plasmid      |52,830 bp    |LexicMap       |63,108     |1,190               |499 s     |4.6 GB  |
 |               |             |Blastn         |69,311     |2,308               |2,262 s   |364.7 GB|
-|1033 AMR genes |1 kb (median)|LexicMap       |3,867,003  |2,228,339           |1,254 s   |21.4 GB |
+|1033 AMR genes |1 kb (median)|LexicMap       |3,867,003  |2,228,339           |4,350 s   |16.3 GB |
 |               |             |Blastn         |5,357,772  |2,240,766           |4,686 s   |442.1 GB|
 
 
+
 AllTheBacteria HQ (1,858,610 genomes):
 
 
 |query          |query_len    |tool           |genome_hits|genome_hits(qcov>50)|time      |RAM     |
-|:--------------|:------------|:--------------|----------:|-------------------:|---------:|-------:|
-|a marker gene  |1,299 bp     |LexicMap       |27,963     |27,953              |41.7 s    |3.4 GB  |
+|:--------------|------------:|:--------------|----------:|-------------------:|---------:|-------:|
+|a marker gene  |1,299 bp     |LexicMap       |27,963     |27,953              |31 s      |3.4 GB  |
 |               |             |Phylign_local  |7,936      |                    |30 m 48 s |77.6 GB |
 |               |             |Phylign_cluster|7,936      |                    |28 m 33 s |        |
-|a 16S rRNA gene|1,542 bp     |LexicMap       |1,857,761  |1,740,000           |13 m 24 s |13.7 GB |
+|a 16S rRNA gene|1,542 bp     |LexicMap       |1,857,761  |1,740,000           |9 m 36 s  |14.9 GB |
 |               |             |Phylign_local  |1,017,765  |                    |130 m 33 s|77.0 GB |
 |               |             |Phylign_cluster|1,017,765  |                    |86 m 41 s |        |
-|a plasmid      |52,830 bp    |LexicMap       |468,821    |3,618               |20 m 48 s |15.9 GB |
+|a plasmid      |52,830 bp    |LexicMap       |468,821    |3,618               |15 m 55 s |15.7 GB |
 |               |             |Phylign_local  |46,822     |                    |47 m 33 s |82.6 GB |
 |               |             |Phylign_cluster|46,822     |                    |39 m 34 s |        |
-|1033 AMR genes |1 kb (median)|LexicMap       |21,288,000 |12,148,642          |168 m 48 s|49.2 GB |
+|1033 AMR genes |1 kb (median)|LexicMap       |21,288,000 |12,148,642          |138 m 55 s|49.9 GB |
 |               |             |Phylign_local  |1,135,215  |                    |156 m 08 s|85.9 GB |
 |               |             |Phylign_cluster|1,135,215  |                    |133 m 49 s|        |
 
 
+
 Genbank+RefSeq (2,340,672 genomes):
 
 |query          |query_len    |tool           |genome_hits|genome_hits(qcov>50)|time      |RAM     |
-|:--------------|:------------|:--------------|----------:|-------------------:|---------:|-------:|
-|a marker gene  |1,299 bp     |LexicMap       |37,164     |37,082              |51.9 s    |4.1 GB  |
-|a 16S rRNA gene|1,542 bp     |LexicMap       |1,949,496  |1,381,974           |13 m 53 s |13.1 GB |
-|a plasmid      |52,830 bp    |LexicMap       |544,619    |6,563               |23 m 30 s |17.5 GB |
-|1033 AMR genes |1 kb (median)|LexicMap       |25,702,419 |14,692,624          |242 m 25 s|56.2 GB |
+|:--------------|------------:|:--------------|----------:|-------------------:|---------:|-------:|
+|a marker gene  |1,299 bp     |LexicMap       |37,164     |37,082              |36 s      |4.1 GB  |
+|a 16S rRNA gene|1,542 bp     |LexicMap       |1,949,496  |1,381,974           |10 m 41 s |14.1 GB |
+|a plasmid      |52,830 bp    |LexicMap       |544,619    |6,563               |19 m 20 s |19.3 GB |
+|1033 AMR genes |1 kb (median)|LexicMap       |25,702,419 |14,692,624          |187 m 40 s|55.4 GB |
+
 
 Notes:
 - All files are stored on a server with HDD disks. No files are cached in memory.

diff --git a/docs/content/[email protected] b/docs/content/[email protected]
@@ -1,5 +1,5 @@
 Query	Genome hits	Time	RAM
-A 1.3-kb marker gene	37,164	52s	4.1 GB
-A 1.5-kb 16S rRNA	1,949,496	13m53s	13.1 GB
-A 52.8-kb plasmid	544,619	23m30s	17.5 GB
-1003 AMR genes	25,702,419	4h02m	41.3 GB
+A 1.3-kb marker gene	37,164	36 s	4.1 GB
+A 1.5-kb 16S rRNA	1,949,496	10 m 41 s	14.1 GB
+A 52.8-kb plasmid	544,619	19 m 20 s	19.3 GB
+1003 AMR genes	25,702,419	187 m 40 s	55.4 GB