INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO:    fuse: warning: library too old, some operations may not work
CNVkit 0.9.9
Detected file format: bed
Splitting large targets
Applying annotations as target names
Detected file format: gff
Wrote ./S07604514_Covered.target.bed with 280504 regions
Detected file format: bed
Wrote ./S07604514_Covered.antitarget.bed with 40780 regions
Building a copy number reference from normal samples...
Processing reads in patient1_normal_DNA_aligned_sort_mkdp.bam
Processing reads in patient1_normal_DNA_aligned_sort_mkdp.bam
concurrent.futures.process._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 142, in _na_arithmetic_op
    result = expressions.evaluate(op, left, right)
  File "/usr/local/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 235, in evaluate
    return _evaluate(op, op_str, a, b)  # type: ignore[misc]
  File "/usr/local/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 69, in _evaluate_standard
    return op(a, b)
TypeError: unsupported operand type(s) for -: 'int' and 'str'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/usr/local/lib/python3.9/site-packages/cnvlib/batch.py", line 157, in batch_write_coverage
    cnarr = coverage.do_coverage(bed_fname, bam_fname, by_count, 0, processes, fasta)
  File "/usr/local/lib/python3.9/site-packages/cnvlib/coverage.py", line 27, in do_coverage
    cnarr = interval_coverages(bed_fname, bam_fname, by_count, min_mapq,
  File "/usr/local/lib/python3.9/site-packages/cnvlib/coverage.py", line 57, in interval_coverages
    table = interval_coverages_pileup(bed_fname, bam_fname, min_mapq,
  File "/usr/local/lib/python3.9/site-packages/cnvlib/coverage.py", line 170, in interval_coverages_pileup
    spans = table.end - table.start
  File "/usr/local/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
    return method(self, other)
  File "/usr/local/lib/python3.9/site-packages/pandas/core/arraylike.py", line 97, in __sub__
    return self._arith_method(other, operator.sub)
  File "/usr/local/lib/python3.9/site-packages/pandas/core/series.py", line 4998, in _arith_method
    result = ops.arithmetic_op(lvalues, rvalues, op)
  File "/usr/local/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 189, in arithmetic_op
    res_values = _na_arithmetic_op(lvalues, rvalues, op)
  File "/usr/local/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 149, in _na_arithmetic_op
    result = _masked_arith_op(left, right, op)
  File "/usr/local/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 91, in _masked_arith_op
    result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'int' and 'str'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/bin/cnvkit.py", line 9, in <module>
    args.func(args)
  File "/usr/local/lib/python3.9/site-packages/cnvlib/commands.py", line 110, in _cmd_batch
    args.reference, args.targets, args.antitargets = batch.batch_make_reference(
  File "/usr/local/lib/python3.9/site-packages/cnvlib/batch.py", line 139, in batch_make_reference
    target_fnames = [tf.result() for tf in tgt_futures]
  File "/usr/local/lib/python3.9/site-packages/cnvlib/batch.py", line 139, in <listcomp>
    target_fnames = [tf.result() for tf in tgt_futures]
  File "/usr/local/lib/python3.9/concurrent/futures/_base.py", line 438, in result
    return self.__get_result()
  File "/usr/local/lib/python3.9/concurrent/futures/_base.py", line 390, in __get_result
    raise self._exception
TypeError: unsupported operand type(s) for -: 'int' and 'str'