 Hi, guys! I am a newbie in pabio sequence analysis ,  recently I download some pacbio RSII data from ncbi sra database, after fastq-dump , I get a fastq file which I think is the raw subread data.

But now I want to do ccs(Circular Consensus Sequence calling) step , the pacbio ccs binary software need the bam or bax (bax can be transformed to bam )file as input ,  also in the sra website , there is no h5 format file submitted by submitter ,  so there only has fastq file , so I don't know how to do with the pacbio fastq file ? Thanks!
Since you say that you are getting Fastq/fasta files, the first step is to correct them. The best way to go about it is to either use Falcon till the generation of preads or Canu's correct-trim mode or use proovread.

If you had the bax/bam files, this would have been easier as you could import them into SMRTlink and you could have used it's pushbutton nature :)