First off, thanks for keeping these files updated!
2nd—I think there might be an issue with the 138.2 .tax or .align files:
When running classify.seqs using freshly downloaded 138.2 files, everything classifies as ‘unknown’.
Same input data behaves normally with the 138.1 .align and .tax files.
Any thoughts here?
Much appreciated!
Can you post an example of one of your sequences? I suspect it’s either backwards or not a 16S rRNA gene sequence.
Pat
Sure, this is aligned with the full-length 138.1 db. Processing is via the MiSeq SOP run as a batch, using a batchfile template that has been working fine for years.
M02808_305_000000000-KTJ3H_1_1101_13739_22372
T-AC–GT-AC-CGT—CCA-A-A—C–G–T—T–AT-T-CGG-AA—TT-A–C-T–GG-GC-----TT–A----AA-GG-GT-AC------G-TA-G-G-C-G—G–C-GC-T-G-T---------CA—G-T-C-G-----G-G-T–G–TG–A-AA-GC–C-C-TC-G-G-----CT-C-AA---------------C-C-G-A-G-G----AAC----T-G–C-G—C–C----C–GA-T-A—C-----T–G-C–AG–T-G-C------------T-T-G-A-G-G–G-----A-GA------CA-G-A---------------G-G-T-A—AG-C----GG–A–ACT-----G-A-T-G-GT–GG-A-G-CG-GT–G-------A–A-A------TG-C-GT-TG–AT-A-TC-------------A-T—C-A------G-G-A-AC-A-CC------AG–T–G–GC-GAA-A–G-C----G-----G–C-T-T-A—CTG------G–GT-C-T-------C-T------A-C-T–GA–CG-----C-----T-G–A-GG–T-A-CG-A–AA-G-C-----T-AG–GG-G–AG-C-G-AA–GG–GG
The strange thing is that this dataset behaved as expected when run with the 138.1 align and tax files; with 633 out of ~250K uniques classifying as unknown. When aligned and classified with 138.2, all ~250K classified as unknown.
Thanks!
-Adam
Resolution on this: Problem was on my side, ran out of HD space when generating the 8mer and prob files in classify seqs. Cleaned up my drive, re-ran and it’s working as it should. Apologies for any time lost thinking about this.
-Adam
wonderful - glad you got it to work
Pat