I have 133 aligned and sorted BAM files that I am trying to run through the ref_map.pl script from the STACKS pipeline. My script looks as follows:

module load stacks

ref_map.pl -T 15 --popmap B2_filenames.txt --samples /home/heather/scratch/03_sort_and_map/filtered_and_sorted/B2/ --out-path /home/heather/scratch/ref_map_results/full_data

echo "ref_map.pl for B2 dataset completed"

I keep running into the issue where gstacks is unable to read the BAM files. This is what the log file looks like:

  Configuration for this run:
  Input mode: reference-based
  Population map: 'B2_filenames.txt'
  Input files: 133, e.g. '/home/heather/scratch/03_sort_and_map/filtered_and_sorted/B2/1401-47750.sort_filt.bam'
  Output to: '/home/heather/scratch/ref_map_results/full_data/'
  Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)

Reading BAM headers...
Processing all loci...
Error: No BAM records.
Error: (At the 0th record in file '/home/heather/scratch/03_sort_and_map/filtered_and_sorted/B2/1401-47754_B2.sort_filt.bam'.)

ref_map.pl: Aborted because the last command failed (1).
Last command executed by ref_map.pl was:
  /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/stacks/2.64/bin/gstacks -I /home/heather/scratch/03_sort_and_map/filtered_and_sorted/B2/ -M B2_filenames.txt -O /home/heather/scratch/ref_map_results/full_data -t 15

I checked the BAM file with samtools - the headers look ok, and I don't get any output when I run samtools quickcheck, so I can't quite figure out what is causing the issue. I am following the same pipeline as I did with a previous batch of data and can't understand whats going wrong.

  • $\begingroup$ "the headers look ok, and I don't get any output when I run samtools quickcheck" - this would be true even if the files contained only headers, no? Do you see alignment info when you look beyond the headers? $\endgroup$
    – Ram RS
    Jul 13 at 18:59
  • $\begingroup$ I keep getting a similar error with the sorted and filtered bam file generated from samtools "Error: 'sample.bam': this is a SAM file (and BAM was specified). $\endgroup$
    – aych
    Jul 18 at 20:32


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