Closed RA-Tsagairt closed 2 years ago
Hi!
I ran a quick test on the master branch and the quantize command you indicate works, so the problem must be elsewhere.
The std::bad_alloc error is a bummer usually, but here are 2 possible causes I can think of:
Hope this helps
Hi!
Thanks for getting back to me. In answer to your questions:
I suspect it has something to do with file paths not being located correctly. I'll try a fresh install and see if that magically solves the issue. I'll let you know how that goes.
Hi!,
Update: It is now working with the fresh installation. Don't know what the issue could have been!
Thanks :)
Great!
Hello,
i have trained several models using your code but they are all really large file sizes. To shrink their memory footprint I am using the command:
python fastDNA/fdna.py -quantize -model_name ~/path_to_model -train_fasta ~/path_to_train_fasta
but it returns the error:
terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) Traceback (most recent call last): File "fastDNA/fdna.py", line 163, in
ft.quantize(model_path, args.train_fasta)
File "fastDNA/python/fastDNA/fastDNA.py", line 67, in quantize
return timed_check_call(command, name=readout, verbose=self.verbose)
File "fastDNA/python/fastDNA/fastDNA.py", line 13, in timed_check_call
subprocess.check_call(command, shell=True)
File "/home/secuser/anaconda3/envs/bio_glove/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'fastDNA/fastdna quantize -input /home/secuser/Rob/bio-predictor-development/fasta_files/25_10_21/train_bf10_C100_L500.fasta -output /home/secuser/Rob/bio-predictor-development/fast_dna/output/models/fdna_k14_d50_e500_lr0.1_n4.0 -qnorm' returned non-zero exit status 134.
I have tried this with various models and their respective training files; all returns the same error. Model sizes are ~20GB.