TypeError: only 0-dimensional arrays can be converted to Python scalars

[jamesdgalbraith]

Hi,

I'm trying to run dysgu and am running into a type error. Do you have any idea how I can remedy this? I've included the log below:

2026-02-24 16:32:25,548 [INFO   ]  [dysgu-call] Version: 1.8.7
2026-02-24 16:32:25,548 [INFO   ]  Input file is: M_producer_adult.bam
2026-02-24 16:32:25,549 [INFO   ]  call --mode pacbio-revio -x -v2 /mnt/loki/ross/assemblies/flies/cecidomyiidae/Aphidoletes_aphidimyza/S_male.ragtag.scaffold.fasta /scratch/jgalbrai/tmp/ M_producer_adult.bam
2026-02-24 16:32:25,727 [WARNING]  Warning: no @RG, using input file name as sample name for output: M_producer_adult
2026-02-24 16:32:25,727 [INFO   ]  Sample name: M_producer_adult
2026-02-24 16:32:25,727 [INFO   ]  Writing vcf to stdout
2026-02-24 16:32:25,727 [INFO   ]  Running pipeline
2026-02-24 16:32:25,730 [INFO   ]  Sequence divergence: 0.02
2026-02-24 16:32:25,734 [INFO   ]  Building cluster graph
2026-02-24 16:32:58,530 [INFO   ]  Total input reads: 2665522
2026-02-24 16:32:58,730 [INFO   ]  Graph constructed
2026-02-24 16:32:58,795 [INFO   ]  Inferred minimum support: 3
Traceback (most recent call last):
  File "/home/jgalbrai/miniforge3/envs/dysgu/bin/dysgu", line 11, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/click/core.py", line 1485, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/click/core.py", line 1406, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/click/core.py", line 1873, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/click/core.py", line 1269, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/click/core.py", line 824, in invoke
    return callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/click/decorators.py", line 34, in new_func
    return f(get_current_context(), *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jgalbrai/miniforge3/envs/dysgu/lib/python3.12/site-packages/dysgu/main.py", line 463, in call_events
    cluster.cluster_reads(ctx.obj)
  File "dysgu/cluster.pyx", line 618, in dysgu.cluster.cluster_reads
  File "dysgu/cluster.pyx", line 402, in dysgu.cluster.pipe1
  File "dysgu/cluster.pyx", line 61, in dysgu.cluster.component_job
  File "dysgu/call_component.pyx", line 2086, in dysgu.call_component.call_from_block_model
  File "dysgu/call_component.pyx", line 2097, in dysgu.call_component.call_from_block_model
  File "dysgu/call_component.pyx", line 2056, in dysgu.call_component.multi
  File "dysgu/call_component.pyx", line 1136, in dysgu.call_component.single
  File "dysgu/call_component.pyx", line 975, in dysgu.call_component.process_spanning
TypeError: only 0-dimensional arrays can be converted to Python scalars

[kcleal]

Hi @jamesdgalbraith,

There is a newer version of dysgu (v1.8.8) which should fix the bug. You can install it using pip, but the conda build is not out yet