qiime2 2019.1 on VM Version 5.2.26.
I'm creating a representative sequence FASTA file in R from a dada2 feature table.
uniquesToFasta(seqtab.nochim, fout='rep-seqs.fna')
This gives me a FASTA file such as:
>sq1;size=9172;
GGAATCGGGATTTCTCATTTCCTGACTAGGGTGATTCTGTCAGCGGTTGATGAATCATTTCACACTCTCTGCTCATTTTGCAATCACTTTTCCACTGCGATCTAAAGCAGATGCTGCAGGTGAGCAAGTATATGCAAGTCCCAGGATGTTGTTTTGTATCCAGAAGGCAGTGGCTGCCTTCCTTCCCCCCTCTTTTGTTGTCCTGGGTGGCAAAAAGCTTCAAGATCTAGCCTTTTCGAATGACAGAGGTTTGGACTGTGTGTTCCAAGTCTGATTTGAAACCAGACAGCTTTTAATATCTGTGAAAATCTGCTGCAGATGTTCAACAAGCAGATTCCCCCTAAAATAAAGCTTTATTCATCCTCCCAGGAAATGGTTCTGCACAGCCAGGAAGAGATACCCCAGTAGTC
>sq2;size=7551;
GGAATCGGGATTTCTCATTTCCTGACTAGGGTGATTCTGTCAGCGGTTGATGAATCATTTCACACTCTCTGCTCATTTTGCAATCACTTTTCCACTGCGATCTAAAGCAGATGCTGCAGGTGAGCAAGTATATGCAAGTCCCAGGATGTTGTTTTGTATCCAGAAGGCAGTGGCTGCCTTCCTTCCCCCCTCTTTTGTTGTCCTGGGTGGCAAAAAGCTTCAAGATCTAGCCTTTTCGAATGACAGAGGTTTGGACTGTGTGTTCCAAGTCTGATTTGAAACCAGACAGCTTTTAATATCTGTGAAAATCTGCTGCAGATGTTCAACAAGCAGATTCCCCCTAAAATAAAGCTTTATTCATCCTCCCAGGAAATGGTTCTGCACAGCCAGGAAGAGATACCCCTGTAGTC
I successfully import this as:
qiime tools import \
--input-path rep-seqs.fna\
--output-path rep-seq.qza \
--type 'FeatureData[Sequence]'
Then I try to run q2-exclude-seqs:
qiime quality-control exclude-seqs \
--i-query-sequences rep-seq.qza \
--i-reference-sequences ../88_otus.qza \
--p-method vsearch \
--p-perc-identity 0.65 \
--p-perc-query-aligned 0.60 \
--p-threads 6 \
--o-sequence-hits hits.qza \
--o-sequence-misses misses.qza \
--verbose
The reference sequences are the greengenes 88_otus and is good as I've successfully used this as recent as q2-2018.11
Then after a few minutes I get an error:
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.Command: vsearch --usearch_global /tmp/qiime2-archive-n8v9h7tt/f2d86460-19ac-4297-937a-123ec4495b91/data/dna-sequences.fasta --id 0.65 --strand both --maxaccepts 1 --maxrejects 0 --db /tmp/qiime2-archive-347oj9gd/cff8af2a-7a2a-4cd2-b45b-91bfc2b971a1/data/dna-sequences.fasta --threads 6 --userfields query+target+ql+qlo+qhi --userout /tmp/tmpgnhe27wx
vsearch v2.7.0_linux_x86_64, 10.2GB RAM, 6 cores
torognes (Torbjørn Rognes) · GitHub vsearch #edited for vanityReading file /tmp/qiime2-archive-347oj9gd/cff8af2a-7a2a-4cd2-b45b-91bfc2b971a1/data/dna-sequences.fasta 100%
15080850 nt in 10544 seqs, min 1258, max 2353, avg 1430
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching query sequences: 2210 of 2863 (77.19%)
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-192>", line 2, in exclude_seqs
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_quality_control/quality_control.py", line 32, in exclude_seqs
perc_query_aligned=perc_query_aligned, method=method)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_quality_control/_blast.py", line 28, in _search_seqs
return _generate_assignments(cmd, perc_query_aligned)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_quality_control/_blast.py", line 67, in _generate_assignments
hits = _extract_hits(output.name, perc_query_aligned)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_quality_control/_blast.py", line 85, in _extract_hits
query_id, subject_id, query_len, start, end = line.split('\t')
ValueError: not enough values to unpack (expected 5, got 1)Plugin error from quality-control:
not enough values to unpack (expected 5, got 1)See above for debug info.
My initial hunch was that there was something amiss with the imported FASTA's description line. The IDs there are automatically created and are uchime-compatible according to the manual. I thought maybe the ;
threw everything off so I tried importing a new FASTA file with the descriptor line exactly the same as the sequences themselves without ;
and I received the same error.
Any help would be appreciated!