Error with salmon quant when filtering alignments by MAPQ

[Taylorain]

Hello,
Thank you for providing and maintaining this fantastic tool!
I am using salmon quant to quantify reads mapped with minimap2, and I encountered an issue when filtering alignments by MAPQ before running salmon quant.

Here is the pipeline I followed:

# Filter reads by quality and length
NanoFilt -q 7 -l 50 ~/fastq/0_A.fa > ~/nanofilt/0_A.filt.fa

# Align reads to reference
minimap2 -ax map-ont -uf -k15 -t 80 --secondary=no ~/drs.fa.idx ~/nanofilt/0_A.filt.fa | samtools view -bS -o 0_A.align.bam 

# Filter alignments by MAPQ >= 1
nohup samtools view -bq 1 -h -@ 80 0_A.align.bam -O bam > 5.0A.filt_bam &

# Quantify with salmon
salmon quant --writeUnmappedNames -t ~/drs.fa --libType A -a 5.0A.filt_bam -o 0_A.salmon.quant --fldMax 200000 -p 64 --ont -g ~/drs.gtf

Issue:

I'm dealing with the quantification of Direct RNA sequencing data.
When I filter the BAM file using samtools view -bq 1, I get an error from salmon quant stating that samtools sort cannot be used, even though I did not use samtools sort in my pipeline.

If I skip filtering alignments by MAPQ (e.g., directly using 0_A.align.bam without the filtering step), the error does not occur.

Questions:

Is there a specific requirement for filtered BAM files used in salmon quant?
How can I correctly filter alignments by MAPQ without encountering this error?
Are there alternative approaches to remove low-quality alignments compatible with salmon quant?

Thank you in advance for your help!