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ValueError: max() arg is an empty sequence in reader.pyx - over a small assembly #29

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atyakhtmpg opened this issue Feb 28, 2023 · 0 comments

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@atyakhtmpg
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Hello, when processing a really small assembly (few contigs each ~1 kbp long) the tool produces an error over this degenerate sample:
File "resmico/reader.pyx", line 118, in resmico.reader.read_contigs_py ValueError: max() arg is an empty sequence

  • apparently failing at
    cdef int max_len = max(py_lengths)
    in reader.pyx, while attempting to get the max of an empty array - the prior log shows:
# Running resmico evaluate
2023-02-27 14:57:42,008 - Loading contig data to verify the range of insert size distribution ...
2023-02-27 14:57:42,008 - Looking for stats/toc files...
2023-02-27 14:57:42,009 - Processing 1 stats/toc files found in <skipped> ...
2023-02-27 14:57:42,009 - Loading feature means and standard deviations from <skipped>/python3.9/site-packages/resmico/model/stats_cov.json
2023-02-27 14:57:42,010 - Found 1 contigs, 0 misassembled, 0 excluded, 1620 total length, 1620 median length, memory needed (assuming fraq-neg=1)   0.00GB
2023-02-27 14:57:42,010 - Breakpoint location histogram: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
2023-02-27 14:57:42,010 - Breakpoint relative position histogram: 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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