test mesh killed

[omarkr8]

not sure where to troubleshoot.

the Identity test worked fine. the mesh test crashed.

_ Database file: 97_shuffled.fa Output file: output2.txt Cores: 2 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: 289 K: 4 Histogram size: 256 A histogram entry is 16 bits. Generating data. Preparing data ... Positive examples: 10000 Training size: 5000 Validation size: 5000 Better performance of: 0.00178729 jeffrey_divergence Better performance of: 0.00169123 jeffrey_divergence simMM Better performance of: 0.00165223 jeffrey_divergence sim_ratio simMM Better performance of: 0.00157806 chi_squared jeffrey_divergence sim_ratio simMM squared_chord^2 x hellinger^2 Better performance of: 0.00154754 chi_squared jeffrey_divergence sim_ratio simMM bray_curtis x hellinger^2 squared_chord^2 x hellinger^2 Better performance of: 0.00151275 chi_squared bray_curtis jeffrey_divergence sim_ratio simMM bray_curtis x hellinger^2 covariance_r x simMM^2 squared_chord^2 x hellinger^2 Better performance of: 0.00147395 chi_squared bray_curtis jeffrey_divergence sim_ratio simMM bray_curtis x jeffrey_divergence bray_curtis x hellinger^2 covariance_r x simMM^2 chi_squared^2 x squared_chord^2 squared_chord^2 x hellinger^2 Selected statistics: chi_squared bray_curtis jeffrey_divergence sim_ratio simMM bray_curtis x jeffrey_divergence bray_curtis x hellinger^2 covariance_r x simMM^2 chi_squared^2 x squared_chord^2 squared_chord^2 x hellinger^2 Finished training. MAE: 0.0217444 MSE: 0.00147395 Optimizing ... Validating ... MAE: 0.0292413 MSE: 0.00208381

Clustering ...

Data run 1 ... Killed_

why would the test fail? could i be lacking some dependencies?

[omarkr8]

tried again with the Identity test fa (keratin_small), and it worked. so something about the test fasta suggested for the mesh tutorial wasnt compatible with my setup?

will try with my own data. perhaps it was data size?

[hani-girgis]

Hi.

To make sure I understand the issue, you cannot cluster 97_shuffled.fa using MeShClust v3.0, correct?

Best

[omarkr8]

correct. I was able to run it using the keratin file, and I am able to run on my own data. but when attempting cluster_97, it kills the process as above