ymilesz
commented
4 years ago Oh I think it is a missing designator error
Closed ymilesz closed 4 years ago
ymilesz
commented
4 years ago Oh I think it is a missing designator error
Hi Brant,
I've successfully completed the phasing UCE tutorial II, and now I want to pull out just SNPs from the phased reads, which I assume uses phyluce_snp_screen_phased_alignments?
However I am getting this error from the tutorial dataset:
[yuanmeng.zhang@login1 all]$ phyluce_snp_screen_phased_alignments --alignments ./multialign-bams-phased-reads/fastas --input-format fasta --output-format phylip --random --output SNP
2020-02-23 01:55:15,429 - phyluce_snp_screen_phased_alignments - INFO - ========= Starting phyluce_snp_screen_phased_alignments ========= 2020-02-23 01:55:15,429 - phyluce_snp_screen_phased_alignments - INFO - Version: git fatal: Not a git repository: '/apps/phyluce/20191015/lib/python2.7/site-packages/.git' 2020-02-23 01:55:15,429 - phyluce_snp_screen_phased_alignments - INFO - Argument --alignments: /ufrc/lucky/yuanmeng.zhang/tutorial/taxon-sets/all/multialign-bams-phased-reads 2020-02-23 01:55:15,429 - phyluce_snp_screen_phased_alignments - INFO - Argument --cores: 1 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --include_missing: False 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --input_format: fasta 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --log_path: None 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --numerical_encoding: False 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --output: /ufrc/lucky/yuanmeng.zhang/tutorial/taxon-sets/all/SNP 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --output_format: phylip 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --random: True 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Argument --verbosity: INFO 2020-02-23 01:55:15,430 - phyluce_snp_screen_phased_alignments - INFO - Getting alignment files 2020-02-23 01:55:15,432 - phyluce_snp_screen_phased_alignments - INFO - Creating phased, SNP-only alignments using 1 cores ProcessingTraceback (most recent call last): File "/apps/phyluce/20191015/bin/phyluce_snp_screen_phased_alignments", line 221, in
main()
File "/apps/phyluce/20191015/bin/phyluce_snp_screen_phased_alignments", line 209, in main
results = map(worker, work)
File "/apps/phyluce/20191015/bin/phyluce_snp_screen_phased_alignments", line 119, in worker
align = AlignIO.read(aln, args.input_format)
File "/apps/phyluce/20191015/lib/python2.7/site-packages/Bio/AlignIO/init.py", line 447, in read
first = next(iterator)
File "/apps/phyluce/20191015/lib/python2.7/site-packages/Bio/AlignIO/init.py", line 394, in parse
for a in i:
File "/apps/phyluce/20191015/lib/python2.7/site-packages/Bio/AlignIO/init.py", line 292, in _SeqIO_to_alignment_iterator
yield MultipleSeqAlignment(records, alphabet)
File "/apps/phyluce/20191015/lib/python2.7/site-packages/Bio/Align/init.py", line 169, in init
self.extend(records)
File "/apps/phyluce/20191015/lib/python2.7/site-packages/Bio/Align/init.py", line 530, in extend
self._append(rec, expected_length)
File "/apps/phyluce/20191015/lib/python2.7/site-packages/Bio/Align/init.py", line 593, in _append
raise ValueError("Sequences must all be the same length")
ValueError: Sequences must all be the same length
The log file isn't showing any errors, so I am not sure what's going on.
Thanks,
Miles