Error: StopIteration

[gevro]

Hi, I'm getting this error. What is the cause of this? Thanks.

singularity run -W /data -B /scratch/projects/bin/deepconsensus/model:/model -B pwd /scratch/projects/bin/deepconsensus/deepconsensus_0.3.1.sif deepconsensus run --batch_size=1024 --batch_zmws=100 --cpus 1 --max_passes 20 --subreads_to_ccs=blah.subreads_to_ccs.0018.bam --ccs_bam=blah.ccs.0018.bam --checkpoint=/model/checkpoint --output=blah.fastq

=================================================================
Total params: 8,942,667
Trainable params: 8,942,667
Non-trainable params: 0
_________________________________________________________________
I0809 10:21:26.338892 140397309962048 model_utils.py:231] Setting hidden size to transformer_input_size.
I0809 10:21:26.339057 140397309962048 quick_inference.py:484] Finished initialize_model.
I0809 10:21:26.339549 140397309962048 quick_inference.py:738] Model setup took 1.790560245513916 seconds.
Traceback (most recent call last):
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/preprocess/utils.py", line 981, in proc_feeder
    ccs_bam_read = next(ccs_bam_h)
  File "pysam/libcalignmentfile.pyx", line 1874, in pysam.libcalignmentfile.AlignmentFile.__next__
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/envs/bio/bin/deepconsensus", line 8, in <module>
    sys.exit(run())
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/cli.py", line 111, in run
    app.run(main, flags_parser=parse_flags)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/cli.py", line 102, in main
    app.run(quick_inference.main, argv=passed)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/share/apps/python/3.8.6/intel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 814, in main
    outcome_counter = run()
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 762, in run
    for zmw, subreads, dc_config in input_file_generator:
  File "/opt/conda/envs/bio/lib/python3.8/site-packages/deepconsensus/inference/quick_inference.py", line 428, in stream_bam
    for input_data in proc_feeder():
RuntimeError: generator raised StopIteration

[danielecook]

@gevro can you confirm that the subreads_to_ccs.bam and ccs.bam files have the same corresponding ZMWs?

Is there any output present in blah.fastq?

[gevro]

I just confirmed by extracting the zmw hole #'s from each, and they are identical. So that can't be the reason. And no fastq file was created.

[danielecook]

@gevro is it possible to share data here so we can examine the issue?

[gevro]

Sure. Do you have a dropbox? Or e-mail address and I can send a link.

[danielecook]

@gevro please email me at my github username @google.com