is it SAM/BAM format?

[gorliver]

I got the following message from fanc pairs:

2024-02-15 23:34:14,038 INFO FAN-C version: 0.9.23
2024-02-15 23:34:14,041 INFO Getting genome regions (fragments or bins)
2024-02-15 23:34:14,041 INFO Getting regions
2024-02-15 23:34:14,045 INFO Three arguments detected, assuming SAM/BAM input.
2024-02-15 23:34:14,047 INFO Using filters appropriate for BWA.
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/threading.py", line 926, in _bootstrap_inner
    self.run()
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/site-packages/fanc/pairs.py", line 171, in _split_sam_worker
    check_sorted=check_sorted):
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/site-packages/fanc/tools/files.py", line 420, in split_sam_pairs
    output_file.write(read.to_string() + '\n')
AttributeError: 'pysam.calignedsegment.AlignedSegment' object has no attribute 'to_string'

Process SpawnPoolWorker-2:
Traceback (most recent call last):
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/multiprocessing/pool.py", line 105, in worker
    initializer(*initargs)
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/site-packages/fanc/pairs.py", line 226, in _load_paired_sam_worker
    for read1, read2 in pair_generator:
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/site-packages/fanc/pairs.py", line 487, in __iter__
    for (read1, read2) in self._iter_read_pairs():
  File "/share/apps/miniconda3/envs/bio/lib/python3.7/site-packages/fanc/pairs.py", line 752, in _iter_read_pairs
    sam = pysam.AlignmentFile(self.sam_file)
  File "pysam/calignmentfile.pyx", line 340, in pysam.calignmentfile.AlignmentFile.__cinit__
  File "pysam/calignmentfile.pyx", line 589, in pysam.calignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_seq=True

The command is:

fanc pairs -f -g references/ge_assembly_100bp.bed -us --bwa -S V35/sam/V35_L1_r1.bam V35/sam/V35_L1_r2.bam V35/pairs/V35_l1.pairs

The bam files were generated using fanc map and everything looked fine.
Any suggestions are highly appreciated.