Hi @rrwick,
thank you for your software, I have been following quick usage pipeline
user manual.
the first two steps no problem:
minimap2 & miniasm.
but when I run minipolish I get issues.
this is my code.
minipolish -t 12 fastq_pass.gz assembly.gfa > polished.gfa
my reads are all in a directory which has been gziped. it wasn't problem for the first two steps, but when I try and use this file for minipolish I have the following errors:
Traceback (most recent call last):
File " /conda_envs/minipolish/bin/minipolish", line 10, in
sys.exit(main())
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/main.py", line 70, in main
initial_polish(graph, args.reads, args.threads, tmp_dir, args.pacbio)
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/main.py", line 83, in initial_polish
save_per_segment_reads(graph, read_filename, tmp_dir)
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/main.py", line 159, in save_per_segment_reads
for read_name, seq, qual in iterate_fastq(read_filename):
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/misc.py", line 78, in iterate_fastq
if get_sequence_file_type(filename) != 'FASTQ':
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/misc.py", line 74, in get_sequence_file_type
raise ValueError('File is neither FASTA or FASTQ')
ValueError: File is neither FASTA or FASTQ
do you know what could be the problem here?
my file only contains fastq reads, but for some reason they are not being recognised at this stage.
thanks in advance.
Hi @rrwick, thank you for your software, I have been following quick usage pipeline user manual.
the first two steps no problem: minimap2 & miniasm. but when I run minipolish I get issues.
this is my code. minipolish -t 12 fastq_pass.gz assembly.gfa > polished.gfa
my reads are all in a directory which has been gziped. it wasn't problem for the first two steps, but when I try and use this file for minipolish I have the following errors:
Traceback (most recent call last): File " /conda_envs/minipolish/bin/minipolish", line 10, in
sys.exit(main())
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/main.py", line 70, in main
initial_polish(graph, args.reads, args.threads, tmp_dir, args.pacbio)
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/main.py", line 83, in initial_polish
save_per_segment_reads(graph, read_filename, tmp_dir)
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/main.py", line 159, in save_per_segment_reads
for read_name, seq, qual in iterate_fastq(read_filename):
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/misc.py", line 78, in iterate_fastq
if get_sequence_file_type(filename) != 'FASTQ':
File " /conda_envs/minipolish/lib/python3.9/site-packages/minipolish/misc.py", line 74, in get_sequence_file_type
raise ValueError('File is neither FASTA or FASTQ')
ValueError: File is neither FASTA or FASTQ
do you know what could be the problem here? my file only contains fastq reads, but for some reason they are not being recognised at this stage. thanks in advance.