UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 1: ordinal not in range(128)

[kerendanan1511]

Hello,

when running rmats.py with these parameters

file=/a/home/cc/lifesci/kerendanan1/provide/high_quality/C017_SCR1Aligned.sortedByCoord.out.bam

output_dir=/a/home/cc/lifesci/kerendanan1/rmats_turbo/provide_rmats/C017_SCR1/rmats

GTF=/a/home/cc/lifesci/kerendanan1/rmats_turbo/gencode.v31lift37.annotation.gtf

python ~/.conda/envs/rmats_env/bin/rmats.py --b1 $file --gtf $GTF -t paired --readLength 150 --nthread 16 --od output_dir --tmp $output_dir/tmp_output --variable-read-length --novelSS --task both

I get this error:

Traceback (most recent call last):
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/bin/rmats.py", line 595, in
main()
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/bin/rmats.py", line 558, in main
args = get_args()
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/bin/rmats.py", line 188, in get_args
args.b1 = fp.read().strip().strip(',')
File "/a/home/cc/lifesci/kerendanan1/.conda/envs/rmats_env/lib/python3.6/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 1: ordinal not in range(128)

Any idea what has gone wrong?

Thanks

[EricKutschera]

Here's the line for that error: https://github.com/Xinglab/rmats-turbo/blob/v4.1.2/rmats.py#L188

The code expects --b1 to be a file with a single line of comma separated bam file paths: https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#starting-with-bam-files

Your command used a bam file directly as --b1 (C017_SCR1Aligned.sortedByCoord.out.bam)

Here's a similar issue: #213 (comment)