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HingeAssembler / HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
http://genome.cshlp.org/content/27/5/747.full.pdf+html?sid=39918b0d-7a7d-4a12-b720-9238834902fd
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Question regarding clipping #115

Closed ebioman closed 7 years ago

ebioman commented 7 years ago

Hi I have a question regarding the work-flow. The minimal example from your Running section succeeds for me. But if I try with a subset from my data I cant get beyond the clip section. Upon running 


Jun  5 09:36 edges.g_out.txt
dgmserv01.vital-it.ch HINGE_00000F hinge clip test.edges.hinges test.hinge.list whatever

Traceback (most recent call last):
  File "/software/UHTS/Assembler/HINGE/20170509/bin/../lib/hinge/pruning_and_clipping.py", line 1357, in 
    add_chimera_flags(G,prefix)
  File "/software/UHTS/Assembler/HINGE/20170509/bin/../lib/hinge/pruning_and_clipping.py", line 1054, in add_chimera_flags
    with open(cov_flags,'r') as f:
IOError: [Errno 2] No such file or directory: 'test.cov.flag'

I guess I have 2 questions related to this

  1. is the identifier-of-run as you put it in the example just a random one which I can choose or should it relate to something from earlier steps in the pipeline?

  2. Indeed the mentioned file test.cov.flag does not exist. At which step should it have been created and what can be the source of it being missing?

I forgot to add, that if I am checking the demo of the ecoli P4, I find a file ecoli.cov.flag which seems to be generated in the first step of filtering, but it is empty.

And indeed I have another file with the extension *.cov.flag in my folder as well but this one corresponds to the hinge layout step -o parameter. If I set though the identifier-of-run similar to the -o parameter it suddenly refers to yet another file...

ilanshom commented 7 years ago

The identifier-of-run doesn't need to be related to any earlier step in the pipeline. It will just be a suffix added to the output files of the clip step.

The .cov.flag file is created in the filter step, and it uses the -x argument for its name. Was that different from test in your case? Also, can you tell us what happens if you create an empty file test.cov.flag and run clip?

ebioman commented 7 years ago

I restarted now the entire hinge steps again from the beginning and gave both, the identifier-of-run and the prefix -x and -o from layout the same name. Everything worked well. If I used another prefix though it always failed to find the correctly associated file.

ilanshom commented 7 years ago

That's good to know, thanks. In the next release of HINGE we will make some changes to prevent this confusion from happening.