Hello everyone,

I used minimap2 to map nanopore direct RNA reads to a genome assembly by the following command:

minimap2 -ax splice -uf -k14 -t80 $refgenome $sample.fastq.gz > test.sam

It was done without any error at all. However, when I try to convert the sam file to a bam file, it suggested a truncated file.

Then I check the file:
wc -l test.sam
456 test.sam

For the successfully transferred file:
wc -l test_success.sam
9151209 test_success.sam

Do you guys have any idea?

Thanks in advanced