bwa-meth unrecognized reference name during sam_parse
Dear all,
I have some Enzymatic methyl sequencing data that I am trying to align using bwa-meth (github.com/brentp/bwa-meth). However, I am encountering the following issue in parsing of the sam file that the aligner is generating when I try to convert the sam file to a bam file.
[W::sam_parse1] unrecognized reference name ""; treated as unmapped
This is the first time for me using bwa-meth tool and I am not able to solve this issue. I am running the following command as suggesting on the GitHub page mentioned above.
bwameth.py --reference ref_genome.fa Sample1_1.fastq.gz Sample1_2.fastq.gz -t 7 | samtools view -b - > sample1.bam
Any help is appreciated.
Thank you.
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