Nicholas Bokulich

Thanks @colinbrislawn ! I have seen the `maxhits` parameter, and I suppose my question could be refined to "what is the difference between maxhits and maxaccepts?" In the example I...

Thanks so much for the explanation, @torognes ! That makes sense re: the `--strand both` option. Version/system info: vsearch v2.7.0_linux_x86_64 CentOS release 6.10

Query Seq: ``` >00009dab2f32e5997c324f5c0822720a GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAAGTTTTTCTGGTGCTTGCACTGGAAAAAACTTAGCGGCGAACGGGTGAGTAACACGTAAAGAACCTGCCTCATAGACTGGGACAACTATTGGAAACGATAGCTAATACCGGATAACAGCATTAACTGCATGGTTGATGTTTGAAAGTTGGTTTTGCTAACACTATGAGATGGCTTTGCGGTGCATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGAAGAAGGATTTCGGGTTCGTAAAGCTCTGTTGTTAGGGAAGAATGATTGTGTAGTAA ``` Ref seqs: ``` >RS_GCF_900476045.1 d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella;s__Gemella morbillorum [locus_tag=NZ_LS483440.1-#4] [location=6886..8440] [ssu_len=1554] [contig_len=1760930] TGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAAGTTTTTCTGGTGCTTGCACTAGAAAAACTTAGCGGCGAACGGGTGAGTAACACGTAAAGAACCTGCCTCATAGACTGGGACAACTATTGGAAACGATAGCTAATACCGGATAACAGTATTTCTCGCATGAGAGATATTTAAAAGTTGGTTATGCTAACACTATGAGATGGCTTTGCGGTGCATTAGCTAGTTGGTGGGGTAAAGGCCCACCAAGGCGACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGAAGAAGGATTTCGGTTCGTAAAGCTCTGTTGTTAGGGAAGAATGGATATGTAGTAACTATACATGTAAGAGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTAATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGTTAAACTTGAGTGCAGGAGAGAAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTTTGGCCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTGGTCTCATAAGAGATCAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAGTCTTGACATACTGTGAGGACACAAGAGATTGTGTTGTTCTGACCTTTGGTTAGACACAGATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATATCTAGTTGCCAGCAGTAAGATGGGGACTCTAGATAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACTTGGGCTACACACGTGCTACAATGGATAGGAACAAAGAGAAGCGAGCTCGCGAGAGTCAGCCAACCTCATAAAACTATTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGACGGTGGCCTAACCTTTAAGGAGGGAGCCGGTCACGGTGGGACAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTC >RS_GCF_001553035.1 d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella;s__Gemella haemolysans_B [locus_tag=NZ_KQ959942.1] [location=53..1607] [ssu_len=1554] [contig_len=1672] AGGAGGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTGTCCCACCGTGACCGGCTCCCTCCTAAAAGGTTAGGCCACCGTCTTCGGGTGTTACAAACTCTCGTGGTGTGACGGGCGGTGTGTACAAGACCCGGGAACGTATTCACCGCGACATTCTGATTCGCGATTACTAGCGATTCCAGCTTCATGTAGTCGAGTTGCAGACTACAATCCGAACTGAGAATAGTTTTGTGAGGTTTGCTTACTCTCGCGAGCTCGCTTCTCTTTGTTCCTATCCATTGTAGCACGTGTGTAGCCCAAGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTATCTAGAGTCCCCATCTTACTGCTGGCAACTAGATATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCATGCACCACCTGTATCTGTGTCTAACCAAAGGTCAGAACAACACAATCTCTTGTGTCCTCACAGTATGTCAAGACTTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTGATCTCTTATGAGACCAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGGCCAAAAAGCCGCCTTCGCCACTGGTGTTCCTCCTAATCTCTACGCATTTCACCGCTACACTAGGAATTCCACTTTTCTCTCCTGCACTCAAGTTTAACAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTATTAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGACAACGCTTGCCACCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGTGGCTTTCTGGTTAGGTACCGTCTCTACTGTGTATAGTTACTACACAATCATTCTTCCCTAACAACAGAGCTTTACGAACCGAAATCCTTCTTCACTCACGCGGCGTTGCTCCGTCAGGCTTTCGCCCATTGCGGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGCATCGTCGCCTTGGTAGGCCTTTACCCCACCAACTAGCTAATGCACCGCAAAGCCATCTCATAGTGTTAGCAAAACCAACTTTTAAACATCAACCATGCAGTTAATGCTGTTATCCGGTATTAGCTATCGTTTCCAATAGTTGTCCCAGTCTATGAGGCAGGTTCTTTACGTGTTACTCACCCGTTCGCCGCTAAGTTTTTCCGGTGCAAGCACCAGAAAAACTTCGCTCGACTTGCATGTATTAGGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAAT ```

Thanks @torognes I am not able to reproduce this with the mini example, but have re-run the original and can confirm that I am getting the same issue with missing...

Hi @torognes I tested in version 2.14.1 and I am getting the same result. ``` $ vsearch --version vsearch v2.14.1_linux_x86_64, 62.9GB RAM, 24 cores $ head $cdir/vsearch-test-out.txt e0f7b19a89bf28b2c37ecbb9450b7aed GB_GCA_003096895.1 97.6...

Greg, didn't we copy all raw data to the taxa assignment github? Or still in the S3 bucket? I know we have these deposited somewhere outside of qiita already... On...

1972 AN On Fri, Feb 12, 2016 at 3:27 PM, Colin Brislawn [email protected] wrote: > Good to know. Once the links are live I will add them post haste! >...

Sorry, finger slip hit send prematurely. 1972 and 1973 are from a study we are working on now. Unpublished but you should include these --- they are good 16S V4...

Yeah... I think the links on the FTP site use a different nomenclature. I dug up the attached document, which should clear things up: it gives the old and new...

Looks like the link won't attach. Here's the relevant text (or email me directly for the table): Eval Framework ID Nature Methods ID Eval Framework Link QIITA ID / Link...