No mapped read in output bam with gff file

[steven-bioinfo]

Hello,

I want to convert my bam file mapped on genomic assembly (bam by bowtie2) to my predicted genes (gff by prokka). Next I want to use this bam as salmon input.

But when i use the mudskipper bulk command line no reads are mapped on the transcriptome.

I thinks, they have a bug when the gff is loading because This information are logged :
2024-04-18T16:04:35Z INFO mudskipper::bam] Number of reference sequences: 0

I also test our gff in tests folder and i have the same results.

mudskipper bulk -t 1 -a mudskipper/tests/NC_002333.2.sam -g mudskipper/tests/NC_002333.2.gff -o demo.bam
[2024-04-18T16:04:35Z INFO  mudskipper] Mudskipper started...
[2024-04-18T16:04:35Z INFO  mudskipper::annotation] reading the gff file and building the tree.
█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ 102/102
[2024-04-18T16:04:35Z INFO  mudskipper::annotation] building the tree
[2024-04-18T16:04:35Z INFO  mudskipper::annotation] Time to build the tree: 6.540013ms
[2024-04-18T16:04:35Z INFO  mudskipper::bam] Number of reference sequences: 0
[2024-04-18T16:04:35Z INFO  mudskipper::bam] thread count: 1
[2024-04-18T16:04:35Z INFO  mudskipper] Mudskipper finished.

When i use the gtf test file reference sequence are detected and sequence are mapped:

mudskipper bulk -t 1 -a mudskipper/tests/NC_002333.2.sam -g mudskipper/tests/NC_002333.2.gtf -o demo.bam
[2024-04-18T16:07:56Z INFO  mudskipper] Mudskipper started...
[2024-04-18T16:07:56Z INFO  mudskipper::annotation] reading the gtf file and building the tree.
█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ 100/100
[2024-04-18T16:07:56Z INFO  mudskipper::annotation] building the tree
[2024-04-18T16:07:56Z INFO  mudskipper::annotation] Time to build the tree: 9.174297ms
[2024-04-18T16:07:56Z INFO  mudskipper::bam] Number of reference sequences: 24
[2024-04-18T16:07:56Z INFO  mudskipper::bam] thread count: 1
[2024-04-18T16:07:56Z INFO  mudskipper] Mudskipper finished.

Regards,

Steven