Hello, FLAMES aligns my reads to the reference genome but during realignment I get this error:
### skip aligning reads to genome 2023-12-07 15:57:35
### read gene annotation 2023-12-07 15:57:35
remove similar transcripts in gene annotation: Counter({'duplicated_transcripts': 765})
### find isoforms 2023-12-07 15:59:27
Traceback (most recent call last):
File "/users/sparthib/flames/python/bulk_long_pipeline.py", line 270, in <module>
bulk_long_pipeline(args)
File "/users/sparthib/flames/python/bulk_long_pipeline.py", line 202, in bulk_long_pipeline
group_bam2isoform(genome_bam, isoform_gff3, tss_tes_stat, "", chr_to_blocks, gene_dict, transcript_to_junctions, transcript_dict, args.genomefa,
File "/users/sparthib/flames/python/sc_longread.py", line 1115, in group_bam2isoform
for c in get_fa(fa_f):
File "/users/sparthib/flames/python/sc_longread.py", line 45, in get_fa
for line in open(fn):
File "/users/sparthib/.conda/envs/FLAMES/lib/python3.10/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
I cloned the flames package from github and this is my environment info:
Hello, FLAMES aligns my reads to the reference genome but during realignment I get this error:
I cloned the flames package from github and this is my environment info:
Any pointers would be appreciated, thank you!