When using minimap2 to map sequencing reads onto a reference, you can use this kind of command (be careful, this is wrong as you will see later):
minimap2 -a -x map-pb test.fastq reference.fasta > minimap.sam |
The command is verbose and prints this kind of information. Note here the WARN%ING:
[M::mm_idx_gen::0.338*0.98] collected minimizers [M::mm_idx_gen::0.464*1.19] sorted minimizers [WARNING] For a multi-part index, no @SQ lines will be outputted. [M::main::0.464*1.19] loaded/built the index for 863 target sequence(s) ...... |
Then, if you try to convert or read this file, you will most problaby get an error. For instance, to convert this SAM file into a BAM format (using samtools), you will get this error message:
[E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 2 [main_samview] truncated file. |
The solution took me a while but is very simple: if you check the help message of minimap2, you will see that the reference should be provided first. So the top command should be:
minimap2 -a -x map-pb reference.fasta test.fastq > minimap.sam |
that is the reference comes first and then the data.
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