I had consensus reads (ccs.bam) from a PacBio sequencing. I used the assembler hifiasm to create an assembly on these CCS. I got five .gfa files. I have transformed .gfa file using bandage and awk command. Contigs from de novo assemblies (.fasta file) were used in standalone blast against reference genome. I have the coordinates which mapped to the reference genome.
I am interested to align .fasta and reference genome using pbmm2
A. Generate index file for reference and reuse it to align reads
$ pbmm2 index xxx.fasta xxx.mmi
B. Align contig yyy.fasta to reference genome file (xxx.mmi)
pbmm2 align xxx.mmi xxx.fasta
However, I am getting this error.
|> 20210517 18:05:07.939 -|- WARN -|- CheckPositionalArgs -|- 0x11a162dc0|| -|- Input is FASTA. Output BAM file cannot be used for polishing with GenomicConsensus!
How to fix this issue.