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Any info for default threshold and mininum read sequence length for meshclust? #19

Open Crispy13 opened 1 year ago

Crispy13 commented 1 year ago

I can't see it in the README and -h of meshclust.

And I got this error:

Database file: all_region_prefixed.fasta
Output file: output1.txt
Cores: 16
Provided threshold: 0.97
Block size for all vs. all: 25000
Block size for reading sequences: 100000
Number of data passes: 10
Can assign all: No

Average: 224
K: 3
Histogram size: 64
A histogram entry is 32 bits.
Generating data.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
Statistician warning at harmonicMeanRSimilarity. A sequence is too short. Similarity is assigned zero.
KmerHistogram: At least one valid segment is required.
Sequence: G
terminate called after throwing an instance of 'std::exception'
  what():  std::exception

I think this was due to short lengths of some sequences. Was it right?

My questions are,

  1. What's the default threshold value?
  2. If it was, what's the minimum length for clustering?

Thank you.

Crispy13 commented 1 year ago

Additionally, -p 100 option didn't work.