SAM read error for BAM file from minimap2

[pdimens]

Hello,

Following the guide on the Syri documentation, when trying to load the alignments into Syri, this error is immediately shot out:

SAM reader - ERROR - Error in reading SAM file: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

The command to generate the alignment was

minimap2 -a -x asm5 -t 10 --MD --eqx reference.fasta query.fasta | samtools sort

Samtools reads the file no problem with samtools view and samtools view -h (or -H). Minimap version:

minimap2 --version
2.26-r1175

[lrauschning]

Hi, thanks for reporting this! Syri uses pysam to read SAM files. Can you check which version of pysam you have installed on your system? you can do this by opening a python command line and typing print(pysam.__version__) after importing pysam with import pysam.

[lrauschning]

Ah also, try calling syri with -F B. Maybe your samtools call is automatically converting the file to BAM format (you can also check by trying to open the file in a text editor).

[pdimens]

Ah, thank you. It seems -F B was the trick.