Aligning in Biscuit with samblaster and samtools

[KChadwick78]

Hi,
I am getting an output error relating to samblaster when trying to align to me reference genome:

samblaster: Inputting from stdin
samblaster: Outputting to stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[gzread] (null)
samblaster: Loaded 172124 header sequence entries.
samblaster: No reads in input SAM file

This is my code:
module load gcc
module load bowtie2/2.4.1
module load samtools/1.16.1
module load samblaster/0.1.26
module load perl/5.30.2

biscuit align /home/chadders/projects/def-frasiert/methyl_seq/ref_genome/Eubalaena_glacialis_HiC.fasta 1151_B_S11_L001-FP.fastq 1151_B_S11_L001-RP.fastq |
samblaster | samtools sort -o my_output.bam -O BAM -

samtools index my_output.bam

I am super new to this and not sure if I have made a misstep in creating the reference index, but the outputs for this all looked ok. I know the fastq files are ok as they ran fine in bismark.

Thanks

[GregoryFaust]

Does your reference genome really have 172,124 contigs? If so, samblaster should still work fine, it's just a question.

It appears as if the input SAM file only has a header and no alignments. Have you checked for that?