Comments (2)
Superseded by #78
from scrnaseq.
@grst : I think this issue might still persist? I just tried to run version 2.1.0 of the pipeline with gzip compressed genome FASTA & GTF files:
[Truncated nextflow console output]
Command executed:
filter_gtf_for_genes_in_genome.py \
--gtf gencode.v42.primary_assembly.basic.annotation.gtf.gz \
--fasta GRCh38.primary_assembly.genome.fa.gz \
-o GRCh38.primary_assembly.genome.fa_genes.gtf
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER":
python: $(python --version | sed 's/Python //g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/root/nextflow-bin/filter_gtf_for_genes_in_genome.py", line 82, in
extract_genes_in_genome(args.fasta, args.gtf, args.output)
File "/root/nextflow-bin/filter_gtf_for_genes_in_genome.py", line 43, in extract_genes_in_genome
seq_names_in_genome = set(extract_fasta_seq_names(fasta))
File "/root/nextflow-bin/filter_gtf_for_genes_in_genome.py", line 34, in extract_fasta_seq_names
for i, header in enumerate(faiter):
File "/root/nextflow-bin/filter_gtf_for_genes_in_genome.py", line 32, in
faiter = (x[1] for x in groupby(fh, is_header))
File "/usr/local/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
from scrnaseq.
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