Comments (4)
Try push the "enter" and see if another log shows up. If it does, it's running. If your input file are huge, it would take a long time.
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Thank you for your quick reply.
I'm sorry there was an error in my expression .
It's not stopped, but I think the speed is way slower compared to your paper's benchmark results or other user.
The input data is about 5Gbps , illumina short paired end reads, server has 2TB memory and 2 * Xeon 8000 series 40cpus .
I tried compiled version and conda version also with/without -w option to run KMCP .
Used database is genbank-viral that is one of KMCP premade database.
07:05:50.199 [INFO] processed queries: 30374219, speed: 0.159 million queries per minute
07:05:50.199 [INFO] 1.6593% (504003/30374219) queries matched
07:05:50.199 [INFO] done searching
07:05:50.199 [INFO] search results saved to: test2
07:05:50.199 [INFO]
07:05:50.199 [INFO] elapsed time: 3h11m18.24440856s
In my guess, KMCP could analyze faster than kraken2, but in some reason it's speed is slow.
I would like to get help, how I can boost speed.
downloaded version : KMCP v0.9.4
command I ran :
../kmcp/kmcp/kmcp search -d genbank-viral.kmcp -1 ERR1018185_fp_hg38_1.fastq.gz -2 ERR1018185_fp_hg38_2.fastq.gz -o test2 -j 20 -w
03:54:31.955 [INFO] kmcp v0.9.4
03:54:31.955 [INFO] https://github.com/shenwei356/kmcp
from kmcp.
The best way is increase the value of -j.
KMCP is far slower than Kraken, as shown in the paper. :(
from kmcp.
Ah sorry for the misunderstanding. strong points is accuracy.
I was confused while reading other issues related with program operation and speed.
Thank you so much.
from kmcp.
Related Issues (20)
- KMCP database building tutorial HOT 3
- Dealing with novel/non-sequenced species HOT 2
- long read metagenomic profiling HOT 2
- suitable for CDS and/or contig taxonomic assignment? HOT 2
- Masking prophages in bacterial genomes before building database as Phanta does HOT 2
- How to specify multiple kmer values HOT 2
- Add a tutorial of detecting specific pathogen in sequencing data HOT 1
- Detecting closest reference in custom DB HOT 4
- Report statistics of matched, unmatched reads HOT 1
- KMCP's MetaPhlAn output doesn't follow the MetaPhlAn file format HOT 3
- [Suggestion] Use score calibration when identifying proviruses and plasmids HOT 2
- ETA missing when building KMCP index HOT 4
- Merge error (number of fields < query index field) HOT 3
- Optimizing KMCP with HumGut HOT 9
- Kmcp profile empty HOT 2
- TODO: save the search result into a serializing binary file for fast downstream parsing HOT 3
- Availability of old gtdb databases? HOT 5
- coverage is greater than 100 HOT 1
- How to profile results only identify 1 species per reference HOT 6
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