Body: <p>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:</p>
  <pre><code>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 &quot;ref_map.pl for B2 dataset completed&quot;
  </code></pre>
  <p>I keep running into the issue where gstacks is unable to read the BAM files. This is what the log file looks like:</p>
  <pre><code>  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'.)
  Aborted.
  
  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
  </code></pre>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-13T18:59:07.677Z
Comments.Text: "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?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-18T20:32:36.023Z
Comments.Text: 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).
Comments.UserDisplayName: aych
Tags: <sam><genomics><genetics>
Title: STACKS ref_map.pl no BAM records
ThreadText: # STACKS ref_map.pl no BAM records
  
  (Asked by: username_0 on 2023-07-12)
  
  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'.)
  Aborted.
  
  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.
  
  **Tags:** sam, genomics, genetics
  
  > **Comments:**
  > **username_1**: "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?  
  > **username_2**: 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).  
  
  ---
  
  ## 0 answers
  
  