Error during smc++ estimate

[g-fabbri]

Hello!

I get this error in the log file while running smc++ estimate. I've run vcf2smc on three different distinguished samples to get the composite likelihood.

--- Logging error ---
Traceback (most recent call last):
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/logging/init.py", line 1085, in emit
msg = self.format(record)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/logging/init.py", line 929, in format
return fmt.format(record)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/logging/init.py", line 668, in format
record.message = record.getMessage()
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/logging/init.py", line 373, in getMessage
msg = msg % self.args
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/numpy/ma/core.py", line 4451, in int
raise MaskError('Cannot convert masked element to a Python int.')
numpy.ma.core.MaskError: Cannot convert masked element to a Python int.
Call stack:
File "/hpc/home/fbbgli1/.conda/envs/smcpp/bin/smc++", line 8, in
sys.exit(main())
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/frontend/console.py", line 28, in main
cmds[args.command].main(args)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/commands/estimate.py", line 47, in main
analysis = Analysis(args.data, args)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/analysis/analysis.py", line 24, in init
if self.npop != 1:
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/analysis/base.py", line 184, in npop
return len(self.populations)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/analysis/base.py", line 72, in populations
return self._pipeline["load_data"].populations
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/data_filter.py", line 34, in getitem
self.run()
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/data_filter.py", line 54, in run
self._results = f(self._results)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/data_filter.py", line 23, in call
return self.run(contigs)
File "/hpc/home/fbbgli1/.conda/envs/smcpp/lib/python3.8/site-packages/smcpp/data_filter.py", line 229, in run
logger.debug(

Can anyone help me out understanding what's the problem? I also attach the complete log files

slurm_33125_smcpp_estim.e.txt
slurm_33125_smcpp_estim.o.txt

.

Thanks,
Giulia

[athenasyarifa]

Hi Giulia,

I also had the same warning in the first and second EM iterations, although my log likelihood still improves with each iteration, and smc++ could still output the final json file. I suspect it might be related to the mask file, because I did not have this warning message when I run with the -c <cutoff> parameter. Did you figure out the solution to this? It might also help to include the command script you ran that outputs this error?

Thanks!
Rifa

[g-fabbri]

Hi Giulia,

I also had the same warning in the first and second EM iterations, although my log likelihood still improves with each iteration, and smc++ could still output the final json file. I suspect it might be related to the mask file, because I did not have this warning message when I run with the -c <cutoff> parameter. Did you figure out the solution to this? It might also help to include the command script you ran that outputs this error?

Thanks! Rifa

Hi Rifa,

No I didn't figure it out and dropped the analysis altogether unfortunately :(