[main_samview] fail to read the header from "111.sam".

[Anees-caas]

I have aligned the Nanopore reads to reference genome command: minimap2 -ax map-ont -t 8 /ref ./111.fastq.gz >111.sam This command generated Sam files. but when I am converting sam to bam samtools view -bS 111.sam > 111.bam I am getting error: fail to read the header from "111.sam". Please assist to solve this issue, Thanks!

[Siadjeu]

Hey, instead of >111.sam, try to run your line code like this: minimap2 -ax map-ont -t 8 /ref ./111.fastq.gz -o 111.sam

[Anees-caas]

Hi, idk why I was getting that error, recently I am using this command it worked minimap2 -ax map-ont -t 8 /ref/genome.fasta ./fastq.gz | samtools sort -o /sorted.bam

[Siadjeu]

Great that you solved it!

[lh3]

Thank you for the help, @Siadjeu! I am closing the issue.