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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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I start from corrected reads, but unzip doesn't work #82

Closed jamescjc123 closed 6 years ago

jamescjc123 commented 7 years ago

hi, i run the falcon from corrected reads(input types is preads), and it works very well. But when i run the falcon_unzip(the input fofn is corrected reads), it doesn't work(Checking existence of /0-rawreads/raw_reads.db), and the 0-rawreads is empty, i want to know how can i run the falcon_unzip from corrected read?

pb-jchin commented 7 years ago

The phasing part of FALCON-Unzip uses the raw sequences that have the proper het-SNP information. It can't do phasing with the error correct reads. You will have to start with the raw sequences so the code can track the raw read through the pipeline.

jamescjc123 commented 7 years ago

thank you for your answers, and the FALCON and FALCON-Unzip all must start with the raw sequences?

rob123king commented 6 years ago

I linked the rawreads folder from the run that created the preads. This progressed it although have an error, it seemed to work and if the preads were generated from that parent folder then should be fine? error now [ERROR]Task Node(3-unzip/reads) failed with exit-code=32512 [INFO]recently_satisfied: set([]) [INFO]Num satisfied in this iteration: 0 [INFO]Num still unsatisfied: 1 [ERROR]Some tasks are recently_done but not satisfied: set([Node(3-unzip/reads)]) [ERROR]ready: set([]) submitted: set([]) Traceback (most recent call last): File "/home/data/bioinf_resources/programming_tools/falcontest/bin/fc_unzip.py", line 11, in <module> load_entry_point('falcon-unzip==0.4.0', 'console_scripts', 'fc_unzip.py')() File "/scratch/cdunn/fork/.git/LOCAL4/lib/python2.7/site-packages/falcon_unzip/mains/start_unzip.py", line 25, in main File "/scratch/cdunn/fork/.git/LOCAL4/lib/python2.7/site-packages/falcon_unzip/unzip.py", line 319, in run File "/scratch/cdunn/fork/.git/LOCAL4/lib/python2.7/site-packages/falcon_unzip/unzip.py", line 195, in unzip_all File "/home/data/bioinf_resources/programming_tools/falcontest/lib/python2.7/site-packages/pypeflow-1.0.0-py2.7.egg/pypeflow/simple_pwatcher_bridge.py", line 273, in refreshTargets self._refreshTargets(updateFreq, exitOnFailure) File "/home/data/bioinf_resources/programming_tools/falcontest/lib/python2.7/site-packages/pypeflow-1.0.0-py2.7.egg/pypeflow/simple_pwatcher_bridge.py", line 339, in _refreshTargets raise Exception(msg) Exception: Some tasks are recently_done but not satisfied: set([Node(3-unzip/reads)])

pb-cdunn commented 6 years ago

Look for stderr somewhere under 3-unzip/reads. The problem would probably pop out at you, whatever it is.