stream read less than specified amount, expected 4, found 0

[TinyTasy]

Dear Longbow team,

Thank you for your great tool! It is very helpful.

Nevertheless, I am running into some problems while using it.

I am trying to annotate a hifi.bam file with longbow annotate /path/to/hifi/.bam -o annotated.bam (thus using the default mas15 model).
However, I am always getting the error:

[INFO 2023-01-19 16:51:46 annotate] Invoked via: longbow annotate /vol/projects/agrinko/PacBio_K562_pilot_17_1_23/data/m64316_230110_175611.hifi_reads.bam -o /vol/projects/agrinko/PacBio_K562_pilot_17_1_23/data/annotated.bam
[INFO 2023-01-19 16:51:46 annotate] Running with 47 worker subprocess(es)
Traceback (most recent call last):
File "/home/agrinko/.local/bin/longbow", line 8, in
sys.exit(main_entry())
File "/home/agrinko/.local/lib/python3.7/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/home/agrinko/.local/lib/python3.7/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/agrinko/.local/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/agrinko/.local/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/agrinko/.local/lib/python3.7/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/agrinko/.local/lib/python3.7/site-packages/longbow/annotate/command.py", line 153, in main
read_count = bam_utils.load_read_count(pbi)
File "/home/agrinko/.local/lib/python3.7/site-packages/longbow/utils/bam_utils.py", line 77, in load_read_count
idx_contents = fmt.parse_stream(f)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 300, in parse_stream
return self._parsereport(stream, context, "(parsing)")
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 312, in _parsereport
obj = self._parse(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 2120, in _parse
subobj = sc._parsereport(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 312, in _parsereport
obj = self._parse(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 2653, in _parse
return self.subcon._parsereport(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 312, in _parsereport
obj = self._parse(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 2726, in _parse
obj = self.subcon._parsereport(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 312, in _parsereport
obj = self._parse(stream, context, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 848, in _parse
return stream_read(stream, length, path)
File "/home/agrinko/.local/lib/python3.7/site-packages/construct/core.py", line 91, in stream_read
raise StreamError("stream read less than specified amount, expected %d, found %d" % (length, len(data)), path=path)
construct.core.StreamError: Error in path (parsing) -> magic
stream read less than specified amount, expected 4, found 0

Is there anything I can do here? It is my first time ever analyzing long-read data, not to speak of mas-iso-seq data.
My conda environment consists of your env.yml file and I am running the job via sbatch on Ubuntu.

I hope this is reproducible enough!

Best wishes,
Tasy

[jonn-smith]

Hi @TinyTasy

This looks like a problem with your bam index. Is it a valid .pbi (PacBio bam index)? A quick fix would be to rerun pbindex on your input bam to regenerate the .pbi file. I suspect after doing that it will work just fine.

[jonn-smith]

Alternatively, you could just move the .pbi file out of the directory containing the bam and it should run.