I tried to examine the Blast classifier for the first time to have its output then compare it to others, but it does not run because of the the comment that I did not understand. I need you to give me a hint why did not it run?
qiime feature-classifier classify-consensus-blast \
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: blastn -query /tmp/qiime2-archive-_23tpuac/e8de5a5c-545a-4917-8e2d-7a8edab2ef6d/data/dna-sequences.fasta -evalue 0.001 -strand plus -outfmt 7 -subject /tmp/qiime2-archive-28b86uag/7fb65b6d-f8ac-4233-a5a9-29d2ca9619dd/data/dna-sequences.fasta -perc_identity 80.0 -qcov_hsp_perc 80.0 -max_target_seqs 10 -out /tmp/tmpou2l_fbc
Also, as you see, I did not use these parameters:
–p-maxaccepts INTEGER Maximum number of hits to keep for each query. Must
Range(1, None) be in range [1, infinity]. BLAST will choose the
first N hits in the reference database that exceed
perc-identity similarity to query. [default: 10]
–p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True)
Reject match if percent identity to query is lower.
Must be in range [0.0, 1.0]. [default: 0.8]
–p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True)
Reject match if query alignment coverage per
high-scoring pair is lower. Note: this uses blastn’s
qcov_hsp_perc parameter, and may not behave
identically to the query-cov parameter used by
classify-consensus-vsearch. Must be in range [0.0,
I would like to know based on what criteria can I determine an appropriate integers for each parameter? Is it OK with default? Or I have to change them according to my project circumstances?