Hello again everyone,
I'm struggling with the outputs of the tool BWA-MEM on my assembly alignement.
I have two input files : - pb_268_p_ctg.fasta : an assembly of my genome, that I want to be polish, that's why I need an alignement - filtered-reads.fastq : my raw reads from PacBio, a almost 90 Gb file
I tried to align my raw reads on my assembly using BWA-MEM in the following way :
./bwa index /path/pb_268_p_ctg.fasta ./bwa mem -x pacbio -t 20 /path/pb_268_p_ctg.fasta /path/filtered_subreads.fastq > /path/falcon_aligned_reads.sam
But the results are very strange. After indexing the sam file, IGV show a very strange message :
File: /media/loutre/SUZUKII/assembly_tries/falcon_aligned_reads.sam does not contain any sequence names which match the current genome. File: null, Genome: 000000F, 000001F, 000002F, 000003F, ...
The sequences name seems to be the same within the assembly file and the sam header file...
Did I missed something ?