qiime feature-classifier classify-consensus-blast

I ran : qiime feature-classifier classify-consensus-blast --i-query dada2_sequences_with_Proteobacteria.qza --i-reference-reads rpoB_ref_2019final.fas.qza --i-reference-taxonomy rpoB_ref_2019final.tax.qza --p-perc-identity 0.977 --p-maxaccepts 1 --p-min-consensus 0.80 --o-classification dada2_sequences_with_Rhizobia_Unassigned_taxonomy.qza

got the error saying :
Plugin error from feature-classifier:Command ‘[‘blastn’, ‘-query’, ‘/tmp/qiime2-archive-bhtms5m7/1913203d-8437-4779-9618-729a56b3fcbc/data/dna-sequences.fasta’, ‘-evalue’, ‘0.001’, ‘-strand’, ‘both’, ‘-outfmt’, ‘7’, ‘-subject’, ‘/tmp/qiime2-archive-ymca94ew/314a426a-96d1-46a2-b1ca-40871918d855/data/dna-sequences.fasta’, ‘-perc_identity’, ‘97.7’, ‘-qcov_hsp_perc’, ‘80.0’, ‘-max_target_seqs’, ‘1’, ‘-out’, ‘/tmp/tmpbx370wpk’]’ returned non-zero exit status 3.

I have no idea what does it mean, I will be really grateful to you if anyone can help me out from this problem.

Hi @amin,

Consulting the blastn manual provides info on these error codes:
https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.Tc/

So error code 3 means “Error in BLAST engine”… a few steps to troubleshoot:

  1. add the “–verbose” flag to your command to see the complete error message
  2. you should probably consult the blastn manual directly to gain more insight into this error. We have not seen this error before, so I suspect may be related to the marker gene you are looking at, and/or the parameter settings…

Please give that a try and let us know what you find.