RuntimeWarining: invalid value encountered in divide

[annezhou94]

Hi,
I was trying to use Bookend to polish the 5UTR annotation of a current annotation file. I did bookend elr and bookend assemble, using default parameters. I encountered this warning message as below:
python3.8/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
python3.8/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in divide
ret = ret.dtype.type(ret / rcount)

It seems the program stopped running when encountered this issue, as there were only 7 assembled transcripts written to bookend_assembly.gtf. Can you help me with this problem? Thank you!

[nextgenusfs]

Same problem.

bookend assemble --max_intron 3000 --min_intron_len 10 --min_len 200 --use_sources 1730-02-09.bam.elr

/| bookend assemble |\
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
  Input file:                                       1730-02-09.bam.elr
  Output file (-o):                                 bookend_assembly.gtf
  Source name (--source):                           bookend
  *** Experiment parameters ***
  Max allowed gap in coverage (--max_gap):          50
  Max end cluster distance (--end_cluster):         100
  Min spanning bases (--min_overhang):              3
  Split read sources (--use_sources):               True
  Ignore end labels (--ignore_labels):              False
  *** Filters ***
  Min bp transcript length (--min_len):             200
  Min isoform coverage (--min_cov):                 2
  Min unstranded coverage (--min_unstranded_cov):   20
  Min isoform contribution (--min_proportion):      0.01
  Min retained intron proportion (--intron_filter): 0.15
  Min number of Start Tags (--min_start):           0
  Min number of End Tags (--min_end):               0
  Min percent 5' end reads w/ uuG (--cap_filter):   0.02
  Score multiplier for Cap Tags (--cap_bonus):      5
  Keep fragmented assemblies (--allow_incomplete):  False

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3372: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/usr/lib/python3/dist-packages/numpy/core/_methods.py:170: RuntimeWarning: invalid value encountered in true_divide
  ret = ret.dtype.type(ret / rcount)
OverflowError: can't convert negative value to char
Exception ignored in: '_assembly_utils.Locus.build_membership_matrix'
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/dist-packages/bookend/core/assemble.py", line 168, in process_entry
    locus = Locus(
OverflowError: can't convert negative value to char

Note that the error changes slightly compared to v1.2.1 (above) versus the current repo (below):

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3372: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/usr/lib/python3/dist-packages/numpy/core/_methods.py:170: RuntimeWarning: invalid value encountered in true_divide
  ret = ret.dtype.type(ret / rcount)
can't convert negative value to char