spladder test yields IndexError: index 0 is out of bounds for axis 0 with size 0

[careenfoord]

• spladder version: 3.0.5
• Python version: 3.10.8
• Operating System: CentOS Linux 7

Description

Hello,
I'm trying to use spladder followed by ribosplitter for plotting isoform and downstream changes in my data.
Spladder Build seemed to function without errors, but when running spladder test I get this error message "IndexError: index 0 is out of bounds for axis 0 with size 0". Does that mean that there's no splicing events in these subsets (these are large files of ~2 million reads) or an underlying error?

What I Did

spladder build --bams *sample.bam --annotation gencode.v34.annotation.gtf --outdir spladder_all_combined
spladder test --conditionA all_L4_young_filtered_header.bam --conditionB all_L4_old_filtered_head.bam --outdir spladder_all_combined/

/home/caf4010/mambaforge/envs/RiboSplitter/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/caf4010/mambaforge/envs/RiboSplitter/lib/python3.10/site-packages/numpy/core/_methods.py:121: RuntimeWarning: divide by zero encountered in divide
  ret = um.true_divide(
/home/caf4010/mambaforge/envs/RiboSplitter/lib/python3.10/site-packages/numpy/core/_methods.py:121: RuntimeWarning: invalid value encountered in divide
  ret = um.true_divide(
Traceback (most recent call last):
  File "/home/caf4010/mambaforge/envs/RiboSplitter/bin/spladder", line 8, in <module>
    sys.exit(main())
  File "/home/caf4010/mambaforge/envs/RiboSplitter/lib/python3.10/site-packages/spladder/spladder.py", line 229, in main
    options.func(options)
  File "/home/caf4010/mambaforge/envs/RiboSplitter/lib/python3.10/site-packages/spladder/spladder_test.py", line 597, in spladder_test
    (cov, psi, gene_idx, event_idx, event_ids, event_samples) = quantify.quantify_from_counted_events(options.fname_event_counts, idx1, idx2, event_type, options, gen_event_ids=False, high_mem=options.high_memory)
  File "/home/caf4010/mambaforge/envs/RiboSplitter/lib/python3.10/site-packages/spladder/alt_splice/quantify.py", line 401, in quantify_from_counted_events
    if samples[0].endswith('npz'):
IndexError: index 0 is out of bounds for axis 0 with size 0

Here are currently loaded packages:

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge _sysroot_linux-64_curr_repodata_hack 3 h69a702a_16 conda-forge anyio 3.7.1 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310ha75aee5_5 conda-forge arrow 1.2.3 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge attrs 24.2.0 pyh71513ae_0 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_4 conda-forge backports.functools_lru_cache 2.0.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge binutils_impl_linux-64 2.39 he00db2b_1 conda-forge binutils_linux-64 2.39 h5fc0e48_13 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.32.3 h4bc722e_0 conda-forge ca-certificates 2024.8.30 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge 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pypi fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge fsspec 2024.9.0 pypi_0 pypi gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge gcc_linux-64 12.2.0 h4798a0e_13 conda-forge genometools-genometools 1.6.4 py310h3db02ab_0 bioconda gettext 0.22.5 he02047a_3 conda-forge gettext-tools 0.22.5 he02047a_3 conda-forge gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge gfortran_linux-64 12.2.0 h307d370_13 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge gxx_linux-64 12.2.0 hb41e900_13 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.11.0 pypi_0 pypi harfbuzz 6.0.0 h8e241bc_0 conda-forge hdf5 1.14.0 nompi_h5231ba7_103 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.8 pyhd8ed1ab_0 conda-forge importlib_resources 6.4.4 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[akahles]

Thanks for reporting - can you share the content of your SplAdder output directory?