Attempting to generate a sam file that can be converted to a bam file using samtools.

Question

[dlera.lozano]

Hi! As the title says I have been trying to generate a bam file using a sam file generated from minimap2. Here is the script I am using to generated the SAM file.

  #Variables
export ASSEMBLY=PATH/BC01_racon3.fasta
export PFX=BC01_BLOB
export READS=PATH/barcode01_trimmed100.fastq

#Commands
PATH/minimap2 -t $SLURM_NTASKS $ASSEMBLY $READS > ${PFX}.sam

Once this file is generated I attempt to use the following:

samtools view -b BC01_BLOB.sam > BC01_BLOB.bam

And I recieve the following error:

[E::sam_parse1] missing SAM header
[W::sam_read1] parse error at line 1
[main_samview] truncated file.

Any help would be greatly appreciated! I just started working in bash recently so I really don't have much experience. I am trying to get a bam file for blobtools.

Answer 1

[GenoMax]

You need to add -a option to create SAM format files to your minimap2 command. By default minimap2 makes PAF format data.

[dlera.lozano]

I think the conversion is running now without issue, Thank you so much!

[GenoMax]

Great. You can accept the answer (green check mark) to provide closure to this thread.