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NCBI Prokaryotic Genome Annotation Pipeline
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[Permanent Failed] WARNING [step prepare_input_template] completed permanentFail #171

Closed minhtrung1997 closed 2 years ago

minhtrung1997 commented 2 years ago

Hi author, I'm new to PGAP and is striving to annotate H.pylori genome. But error of Permanent Fail is still recurrent. It's a bit disappointed as I try a way to fix bug my self. I've tried test file from genome test but None complete, either.

Could you please take a glance at those input and log files and give us recommendations Thanks PS: I run PGAP on Linux Ubuntu RAM 32 GB and 251GB Disk. CPU is Intel® Xeon(R) CPU E5-2620 0 @ 2.00GHz × 24 cwltool.log Test.yaml.txt Test_submol.yaml.txt

azat-badretdin commented 2 years ago

Thank you for your report, user minhtrung1997. The log file contains indication to an error in the input:

member authors expected

At this moment it is not clear why the YAML(JSON) parser complains about this field. We will take a look at your input.

minhtrung1997 commented 2 years ago

I send you an assembly file. Please check it. For I have an incoming project, so please help me soon. Thanks assembly.txt

azat-badretdin commented 2 years ago

Thanks!

azat-badretdin commented 2 years ago

I am back. The problem was in the typo in the word "topology" (it was "toplogy") after I fixed it the node that was failing was able to read through this place in code.

We are investigating why our JSON parser reported a completely unrelated problem.

Hopefully this typo fix will allow you to move ahead with your genome