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khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics
http://www.recentrifuge.org
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More than 10 mins on a centrifuge result (21.3 MB) #26

Closed yeli7068 closed 4 years ago

yeli7068 commented 4 years ago

Hi,

The latest version (v1.2.1) took more than 10 mins on a small result. ion_test.fq.zip The input was a centrifuge result as attached (21.3 MB after decompressing).

Python: Python 3.6.10 :: Anaconda, Inc. Centrifuge: 1.0.4 Hardware: CPU 24C/48T, 128 GB RAM.

Thanks in advance for your helps.

khyox commented 4 years ago

It took exactly 20 seconds (of those, just 1.4 seconds loading the file) on my >1yo laptop with Python 3.8.3, so it should very probably be a local problem with your system/configuration. This is the output:

(...)
Loading output file /Users/user/Downloads/test/ion_test.fq.centri_out... OK!
  Seqs read: 430_839    [70.05 Mnt]
  Seqs clas: 419_293    (2.68% unclassified)
  Seqs pass: 419_293    (0.00% rejected)
  Scores: min = 23.0, max = 261.0, avr = 108.2
  Length: min = 30 nt, max = 365 nt, avr = 163 nt
  TaxIds: by classifier = 15, by filter = 15
Building from raw data with mintaxa = 6 ... 
  Check for more seqs lost ([in/ex]clude affects)... OK!
/Users/user/Downloads/test/ion_test.fq sample OK!
Load elapsed time: 1.39 sec

Building the taxonomy multiple tree... OK!
Generating final plot (GH_TEST.rcf.html)... OK!
Generating Excel full summary (GH_TEST.rcf.xlsx)... OK!
Total elapsed time: 00:00:20

Process finished with exit code 0

I would suggest you to talk to your system administrator so that he/she can be aware of the issue.