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Issues with 'annotate' and 16-element arrays #208

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hdm-23 opened this issue Oct 19, 2023 · 0 comments
Open

Issues with 'annotate' and 16-element arrays #208

hdm-23 opened this issue Oct 19, 2023 · 0 comments

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@hdm-23
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hdm-23 commented Oct 19, 2023

Hi all,

New longbow user here. Hoping to use to annotate/segment cDNAs from a 16-element 3' array with longbow version 0.5.37 and running into issues when specifying -m/--model. It doesn't appear that a mas16 models are available with 0.5.37, but I'm providing a mas16 model manually (which I copied from the docs here). Annotate runs smoothly if I specify a model name from 'longbow model' and if I provide a custom mas15.json model. Output is below:

[INFO 2023-10-19 09:33:29 annotate] Invoked via: longbow annotate XYRWR_20230901_R84050_PL100305584-1_D01.hifi_reads.default_downSam.bam -m mas16_10x3p.json -o test.bam
[INFO 2023-10-19 09:33:29 annotate] Running with 31 worker subprocess(es)
Traceback (most recent call last):
File "/home/mhale/.conda/envs/python37/bin/longbow", line 8, in
sys.exit(main_entry())
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/longbow/annotate/command.py", line 126, in main
lb_models = bam_utils.load_models(model, input_bam)
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/longbow/utils/bam_utils.py", line 227, in load_models
lb_models.append(LibraryModel.from_json_file(model))
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/longbow/utils/model.py", line 1335, in from_json_file
return LibraryModel.from_json_obj(json_data)
File "/home/mhale/.conda/envs/python37/lib/python3.7/site-packages/longbow/utils/model.py", line 1361, in from_json_obj
version=json_data["version"],
KeyError: 'version'

Thanks.

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