Consensus step - empty output about dbg2olc HOT 4 CLOSED

Hi Seyhan,
Yes, this is the case. By default the consensus part needs certain coverage to avoid the erroneous paths. If you really need to proceed with such low coverage, you will need to lower the 'c' parameter to 1.

So maybe try a command like this to see if the error disappears:
Sparc b Backbone.fa m backbone.mapped.m5 k 1 g 1 c 1 t 0.1 o ConsensusOutput

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Thank you, Chengxi. I set the parameters as you suggested and I think it worked. I got the following output message for 12 chunks I tested.

[INFO] 2017-05-04T11:59:56 [blasr] started.
[INFO] 2017-05-04T11:59:57 [blasr] ended.
For help: Sparc -h
Backbone size: 116179
Finished.

Unfortunately, I have to work with what we have. It is going to be interesting to see how much improvement there is going to be.

I have another question. The blasr and sparc steps are set to iterate twice in the original script of 'split_and_run_sparc.sh'. I had to modify this script to run on our cluster so I removed the iteration. Do you think should I bring it back?

Thank you,
Seyhan

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I have never tested on so low coverage and I think it is possible to get slight improvements to bring it back.

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Thank you. I will let you know how it goes

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