UnicodeDecodeError

[igonzals]

Using BRIE v2.2.2, I'm getting this error when I use brie-count:

brie-count -p 12 -o ../brie -a ../stringtie2/merged_transcriptome.gtf -S ../data/bam-trimmed/SRR4047245_Aligned.sortedByCoord.out.bam ../data/bam-trimmed/SRR4047246_Aligned.sortedByCoord.out.bam ../data/bam-trimmed/SRR4047247_Aligned.sortedByCoord.out.bam ../data/bam-trimmed/SRR4047248_Aligned.sortedByCoord.out.bam ../data/bam-trimmed/SRR4047249_Aligned.sortedByCoord.out.bam ../data/bam-trimmed/SRR4047250_Aligned.sortedByCoord.out.bam ../data/bam-trimmed/SRR4047251_Aligned.sortedByCoord.out.bam

Traceback (most recent call last): File "/home/grad17/igonzalez/.local/bin/brie-count", line 33, in sys.exit(load_entry_point('brie==2.2.2', 'console_scripts', 'brie-count')()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/grad17/igonzalez/.local/lib/python3.11/site-packages/brie/bin/count.py", line 303, in main smartseq_count(options.gff_file, options.samList_file, options.out_dir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/grad17/igonzalez/.local/lib/python3.11/site-packages/brie/bin/count.py", line 26, in smartseq_count sam_table = np.loadtxt(samList_file, delimiter = None, dtype=str, ndmin = 2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/site-packages/numpy/lib/npyio.py", line 1356, in loadtxt arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/site-packages/numpy/lib/npyio.py", line 1026, in _read next_arr = _load_from_filelike( ^^^^^^^^^^^^^^^^^^^^ File "", line 322, in decode UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

[huangyh09]

Hi, for -S option, you should input a file listing your bam files, e.g., https://github.com/huangyh09/brie-tutorials/blob/main/tests/run_demo.sh#L24

Yuanhua