BEERS2 failed at the library preparation step

[yihangs]

Hi!

I use CAMPAREE to simulate molecule files and then use BEERS2 to simulate fastq files. I choose "from distribution data" in library_prep_pipeline. BEERS2 failed at very early stage with the following error:

Traceback (most recent call last):
  File "/mnt/ENCFF075XPF_BEERS2_results/.snakemake/scripts/tmp_panbnhd.run_library_prep_pipeline.py", line 38, in <module>
    LibraryPrepPipeline.main(
  File "/mnt/miniconda3/envs/py311/lib/python3.11/site-packages/beers/library_prep/library_prep_pipeline.py", line 273, in main
    molecule_packets = list(molecule_maker.execute(
                            ^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/miniconda3/envs/py311/lib/python3.11/site-packages/camparee/molecule_maker.py", line 427, in execute
    self.isoform_quants = self.load_isoform_quants(psi_quant_path)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/miniconda3/envs/py311/lib/python3.11/site-packages/camparee/molecule_maker.py", line 197, in load_isoform_quants
    for line in isoform_quant_file:
  File "<frozen codecs>", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf0 in position 7: invalid continuation byte

Do you know what the issue is?

Thanks!

[tgbrooks]

Hi Yihangs,

Looks like the file isn't in valid UTF-8 for some reason. Is it possible that any of the annotations or sample names used were not utf-8? You can try running grep -a -n "$(printf '\xF0')" intron_quantifications.txt to identify the problematic line. Or please share the intron_quantifications.txt here (you can email it to me). These will be in the CAMPAREE output directory, one for each sample.

[yihangs]

Thanks! Indeed the issue comes from bad quantification files. I rerun CAMPAREE for these samples to generate new quantification files and run BEERS2 again. It looks good now.