can't decode byte 0x8b in position 1: invalid start byte

[Ali Yavuz Cakir]

I wanted to try Monopogen on my GEX-cellranger output, first started with preprocess.py, however, it directly gave me the following error;

Traceback (most recent call last):
File "/path/Monopogen/src/Monopogen.py", line 435, in
main()
File "/path/Monopogen/src/Monopogen.py", line 428, in main
args.func(args)
File "/path/Monopogen/src/Monopogen.py", line 291, in preProcess
for line in f_in:
File "/miniconda3/lib/python3.9/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

My BAM file is not gzipped, I even tested with different BAM files but the result was the same, I looked into the source code and saw that it tries to open a BAM file with "with open" and seems like it causes the error, can you please help regarding this one?

[JinzhuangDou]

Hi, Monopogen uses the function pysam.AlignmentFile to load the bam files. The open function opens the bam file list (not the bam files). Would you mind share with me a subset of your bam files so that I can examine what happens inside?

[Ali Yavuz Cakir]

Hi, Monopogen uses the function pysam.AlignmentFile to load the bam files. The open function opens the bam file list (not the bam files). Would you mind share with me a subset of your bam files so that I can examine what happens inside?

Oh my bad, I somehow thought I could input a bam file directly :/ Now I tried with a .lst file and then worked! Thank you for your reply!