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This repository was archived by the owner on Oct 18, 2024. It is now read-only.
This repository was archived by the owner on Oct 18, 2024. It is now read-only.

bam test data #141

@bernt-matthias

Description

@bernt-matthias

Hi

I'm trying to fix the galaxy tool for pycoQC for BAM input (galaxyproject/tools-iuc#5201). Wondering if you have input data that is supposed to work?

With the input data I'm using I get:

Job in error state.. tool_id: pycoqc, exit_code: 1, stderr: Checking arguments values
Check input data files
Parse data files
Merge data
Cleaning data
	Discarding lines containing NA values
		0 reads discarded
	Filtering out zero length reads
		0 reads discarded
	Sorting run IDs by decreasing throughput
		Run-id order ['2bf3a5a5424e9267975cff54d2d8d1731fde919f']
	Reordering runids
		Processing reads with Run_ID 2bf3a5a5424e9267975cff54d2d8d1731fde919f / time offset: 0
	Cast value to appropriate type
	Reindexing dataframe by read_ids
		9 Final valid reads
WARNING: Low number of reads found. This is likely to lead to errors when trying to generate plots
Loading plotting interface
	Found 9 total reads
	Found 9 pass reads (qual >= 7.0 and length >= 0)
Generating HTML report
	Parsing html config file
	Running method run_summary
		Computing plot
	Running method basecall_summary
		Computing plot
	Running method alignment_summary
/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3257: RuntimeWarning:

Mean of empty slice.

/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py:161: RuntimeWarning:

invalid value encountered in double_scalars

		Computing plot
	Running method read_len_1D
		Computing plot
	Running method align_len_1D
		Computing plot
Traceback (most recent call last):
  File "/usr/local/bin/pycoQC", line 10, in <module>
    sys.exit(main_pycoQC())
  File "/usr/local/lib/python3.7/site-packages/pycoQC/__main__.py", line 132, in main_pycoQC
    quiet = args.quiet)
  File "/usr/local/lib/python3.7/site-packages/pycoQC/pycoQC.py", line 160, in pycoQC
    skip_coverage_plot=skip_coverage_plot)
  File "/usr/local/lib/python3.7/site-packages/pycoQC/pycoQC_report.py", line 89, in html_report
    fig = method(**method_args)
  File "/usr/local/lib/python3.7/site-packages/pycoQC/pycoQC_plot.py", line 489, in align_len_1D
    height=height)
  File "/usr/local/lib/python3.7/site-packages/pycoQC/pycoQC_plot.py", line 535, in __1D_density_plot
    lab1, dd1, ld1 = self.__1D_density_data ("all", field_name, x_scale, nbins, smooth_sigma)
  File "/usr/local/lib/python3.7/site-packages/pycoQC/pycoQC_plot.py", line 582, in __1D_density_data
    min = np.nanmin(data)
  File "<__array_function__ internals>", line 6, in nanmin
  File "/usr/local/lib/python3.7/site-packages/numpy/lib/nanfunctions.py", line 320, in nanmin
    res = np.fmin.reduce(a, axis=axis, out=out, **kwargs)
ValueError: zero-size array to reduction operation fmin which has no identity
.

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