PBAlign for Quiver doesn't work for targeted input.fofn

[juckdnarocks]

I extracted target reads from bax.h5 files and got rgn.h5 files. But these rgn.h5 file cann't be used to generate cmp.h5 files with the script pbalign for quvier.
Here is the error message
"2015-04-21 16:00:55,739 [ERROR] Neither the input file is in bas/pls/ccs.h5 format, nor --pulseFile is specified, , while --forQuiver is true."
But the input file is rgn.h5 files which contain pulses.

Thanks in advance.

[gconcepcion]

I extracted target reads from bax.h5 files and got rgn.h5 files. But these rgn.h5 file cann't be used to generate cmp.h5 files with the script pbalign for quvier.
Here is the error message
"2015-04-21 16:00:55,739 [ERROR] Neither the input file is in bas/pls/ccs.h5 format, nor --pulseFile is specified, , while --forQuiver is true."
But the input file is rgn.h5 files which contain pulses.

Thanks in advance.

rgn.h5's don't contain any sequence data, which is why they cannot be used with pbalign to generate alignments. They only provide positional information (thread by the author here: http://seqanswers.com/forums/showthread.php?t=30439).
Alignments can only be generated from sequence containing h5 files: *.ccs.h5, *.bas.h5, *.bax.h5 and *.pls.h5

How did you 'extract' the reads from the original bax.h5? What exactly are you trying to accomplish? Just mapping your sequences to a reference? I'm unsure as to the nature of your data and why you needed to 'extract' the target reads first. Why don't you just map your original bax.h5 to a reference containing only target sequences of interest using SMRTPortal && RS_Resequencing.1 protocol?