Skip to content

ValueError: Cannot have only N wildcards in the sequence #42

Description

@realzhang

cat barcodes_for_ultraplex.csv
AAACATNNNNNNNNNN:WT1h1,
ATATGANNNNNNNNNN:WT1h2,
TAAAACNNNNNNNNNN:KR181h1,
TTAACTNNNNNNNNNN:KR181h2,
GGACATNNNNNNNNNN:KR431h1,
CCCCACNNNNNNNNNN:KR431h2,
CGTCGCNNNNNNNNNN:WTno4sU,

The output is:

Namespace(inputfastq='4sU-1h_BRB_raw_1.fq.gz', barcodes='barcodes_for_ultraplex.csv', directory='out.ultraplex', fiveprimemismatches=1, threeprimemismatches=0, phredquality=30, threads=4, adapter='AGATCGGAAGAGCGGTTCAG', outputprefix='demux', sbatchcompression=False, ultra=False, ignore_space_warning=False, final_min_length=20, phredquality_5_prime=0, input_2='4sU-1h_BRB_raw_2.fq.gz', adapter2='AGATCGGAAGAGCGTCGTG', min_trim=3, ignore_no_match=False, dont_build_reference=False, keep_barcode=False)Demultiplexing...
Process WorkerProcess-1:
Traceback (most recent call last):
File "/home/zhang/mambaforge/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/zhang/mambaforge/lib/python3.9/site-packages/ultraplex/main.py", line 651, in run
read2 = remove_mate_adapter(read=read2,
File "/home/zhang/mambaforge/lib/python3.9/site-packages/ultraplex/main.py", line 786, in remove_mate_adapter
adapter = [BackAdapter(remove_rc, max_error_rate=0.1, min_overlap=2)]
File "/home/zhang/mambaforge/lib/python3.9/site-packages/ultraplex/adapters.py", line 484, in init
super().init(*args, **kwargs)
File "/home/zhang/mambaforge/lib/python3.9/site-packages/ultraplex/adapters.py", line 387, in init
self.aligner = self._aligner()
File "/home/zhang/mambaforge/lib/python3.9/site-packages/ultraplex/adapters.py", line 487, in _aligner
return self._make_aligner(Where.ANYWHERE.value if self._force_anywhere else Where.BACK.value)
File "/home/zhang/mambaforge/lib/python3.9/site-packages/ultraplex/adapters.py", line 394, in _make_aligner
return align.Aligner(
File "ultraplex/_align_new.pyx", line 229, in _align_new.Aligner.cinit
File "ultraplex/_align_new.pyx", line 274, in _align_new.Aligner._set_reference
ValueError: Cannot have only N wildcards in the sequence

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions