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google / deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
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Error detecting params.json using docker in debian (10) HPC #55

Closed ap1438 closed 1 year ago

ap1438 commented 1 year ago

docker run google/deepconsensus:1.1.0 deepconsensus run --subreads_to_ccs=m54274Ue_220814_163631.aligned.subreads.bam --ccs_bam=m54274Ue_220814_163631.hifi_S3_reads.bam --checkpoint=model/checkpoint --output=m54274Ue_220814_163631_deepcon.output.fastq Traceback (most recent call last): File "/opt/conda/envs/bio/bin/deepconsensus", line 8, in sys.exit(run()) File "/opt/conda/envs/bio/lib/python3.9/site-packages/deepconsensus/cli.py", line 111, in run app.run(main, flags_parser=parse_flags) File "/opt/conda/envs/bio/lib/python3.9/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/envs/bio/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/opt/conda/envs/bio/lib/python3.9/site-packages/deepconsensus/cli.py", line 102, in main app.run(quick_inference.main, argv=passed) File "/opt/conda/envs/bio/lib/python3.9/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/envs/bio/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/opt/conda/envs/bio/lib/python3.9/site-packages/deepconsensus/inference/quick_inference.py", line 842, in main outcome_counter = run() File "/opt/conda/envs/bio/lib/python3.9/site-packages/deepconsensus/inference/quick_inference.py", line 703, in run params = model_utils.read_params_from_json(checkpoint_path=FLAGS.checkpoint) File "/opt/conda/envs/bio/lib/python3.9/site-packages/deepconsensus/models/model_utils.py", line 405, in read_params_from_json json.load(tf.io.gfile.GFile(json_path, 'r'))) File "/opt/conda/envs/bio/lib/python3.9/json/init.py", line 293, in load return loads(fp.read(), File "/opt/conda/envs/bio/lib/python3.9/site-packages/tensorflow/python/lib/io/file_io.py", line 116, in read self._preread_check() File "/opt/conda/envs/bio/lib/python3.9/site-packages/tensorflow/python/lib/io/file_io.py", line 77, in _preread_check self._read_buf = _pywrap_file_io.BufferedInputStream( tensorflow.python.framework.errors_impl.NotFoundError: model/params.json; No such file or directory

I am getting this error even though i have all the files from model checkpoint.data-00000-of-00001 checkpoint.index params.json in the model dir.

pichuan commented 1 year ago

Hi @ap1438 , given that you're using Docker, you'll need to make sure the paths you passed in are visible through Docker. The flag you'll need to add is -v. For example, in this section https://github.com/google/deepconsensus/blob/r1.1/docs/quick_start.md#running-the-docker-image , you can see that this flag was added -v "${QS_DIR}":/data.

https://docs.docker.com/storage/volumes/ might also be helpful to read.

ap1438 commented 1 year ago

It worked. Thankyou