# Problems in ''classify.seqs" **URL:** \ **Category:** Commands in mothur\ **Created:** [April 19, 2017, 4:13pm UTC](https://forum.mothur.org/t/problems-in-classify-seqs/3218 "2017-04-19T16:13:30Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Liyang](https://avatars.discourse-cdn.com/v4/letter/l/ed8c4c/32.png) [@Liyang](https://forum.mothur.org/u/Liyang)\ **Post date:** [April 19, 2017, 4:13pm UTC](https://forum.mothur.org/t/problems-in-classify-seqs/3218/1 "2017-04-19T16:13:30Z")
Followed Miseq SOP, “classify.seqs” was to remove the "“undesirable” sequence in our dataset. mothur\>classify.seqs(fasta=_.fasta,count=_.count\_table,reference=silva.gold.ng.fasta,taxonomy=silva.bacteria.silva.tax,cutoff=80) Z14096.1 is in your taxonomy file and is not in your template file. Please corre ct. Z21936.1 is in your taxonomy file and is not in your template file. Please corre ct. Z21979.1 is in your taxonomy file and is not in your template file. Please corre ct. Z22781.1 is in your taxonomy file and is not in your template file. Please corre ct. Z23157.1 is in your taxonomy file and is not in your template file. Please corre ct. Z23158.1 is in your taxonomy file and is not in your template file. Please corre ct. Z23160.1 is in your taxonomy file and is not in your template file. Please corre ct. Z25741.1 is in your taxonomy file and is not in your template file. Please corre ct. Z25742.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26315.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26921.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26922.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26923.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26926.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26927.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26932.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26935.1 is in your taxonomy file and is not in your template file. Please corre ct. Z26939.1 is in your taxonomy file and is not in your template file. Please corre ct. Z29975.1 is in your taxonomy file and is not in your template file. Please corre ct. Z30542.1 is in your taxonomy file and is not in your template file. Please corre ct. Z31657.1 is in your taxonomy file and is not in your template file. Please corre ct. Z31658.1 is in your taxonomy file and is not in your template file. Please corre ct. Z32636.1 is in your taxonomy file and is not in your template file. Please corre ct. Z35304.1 is in your taxonomy file and is not in your template file. Please corre ct. Z35305.1 is in your taxonomy file and is not in your template file. Please corre ct. Z35435.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36272.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36273.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36296.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36925.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36926.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36927.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36928.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36929.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36930.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36933.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36934.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36935.1 is in your taxonomy file and is not in your template file. Please corre ct. Z36936.1 is in your taxonomy file and is not in your template file. Please corre ct. Z37136.1 is in your taxonomy file and is not in your template file. Please corre ct. Z37150.1 is in your taxonomy file and is not in your template file. Please corre ct. Z37151.1 is in your taxonomy file and is not in your template file. Please corre ct. Z37989.1 is in your taxonomy file and is not in your template file. Please corre ct. Z38003.1 is in your taxonomy file and is not in your template file. Please corre ct. Z38007.1 is in your taxonomy file and is not in your template file. Please corre ct. Z38018.1 is in your taxonomy file and is not in your template file. Please corre ct. Z38020.1 is in your taxonomy file and is not in your template file. Please corre ct. Z38023.1 is in your taxonomy file and is not in your template file. Please corre ct. Z46664.1 is in your taxonomy file and is not in your template file. Please corre ct. Z46750.1 is in your taxonomy file and is not in your template file. Please corre ct. Z46751.1 is in your taxonomy file and is not in your template file. Please corre ct. Z46752.1 is in your taxonomy file and is not in your template file. Please corre ct. Z46753.1 is in your taxonomy file and is not in your template file. Please corre ct. Z46754.1 is in your taxonomy file and is not in your template file. Please corre ct. Z47544.1 is in your taxonomy file and is not in your template file. Please corre ct. Z49117.1 is in your taxonomy file and is not in your template file. Please corre ct. Z49264.1 is in your taxonomy file and is not in your template file. Please corre ct. Z49738.1 is in your taxonomy file and is not in your template file. Please corre ct. Z49830.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68095.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68096.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68097.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68098.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68099.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68100.1 is in your taxonomy file and is not in your template file. Please corre ct. Z68101.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70001.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70002.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70004.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70005.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70006.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70007.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70008.1 is in your taxonomy file and is not in your template file. Please corre ct. Z70248.1 is in your taxonomy file and is not in your template file. Please corre ct. Z71365.1 is in your taxonomy file and is not in your template file. Please corre ct. Z73313.1 is in your taxonomy file and is not in your template file. Please corre ct. Z73631.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76651.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76652.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76653.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76654.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76655.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76658.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76659.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76660.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76663.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76665.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76666.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76667.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76669.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76671.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76672.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76673.1 is in your taxonomy file and is not in your template file. Please corre ct. Z76675.1 is in your taxonomy file and is not in your template file. Please corre ct. Z78203.1 is in your taxonomy file and is not in your template file. Please corre ct. Z78204.1 is in your taxonomy file and is not in your template file. Please corre ct. Z78206.1 is in your taxonomy file and is not in your template file. Please corre ct. Z83204.1 is in your taxonomy file and is not in your template file. Please corre ct. Z83205.1 is in your taxonomy file and is not in your template file. Please corre ct. Z94012.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95707.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95708.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95709.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95710.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95711.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95712.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95713.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95714.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95715.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95716.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95717.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95718.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95719.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95720.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95721.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95722.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95723.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95724.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95725.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95726.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95727.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95728.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95729.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95730.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95731.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95732.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95733.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95734.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95735.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95736.1 is in your taxonomy file and is not in your template file. Please corre ct. Z95737.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96077.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96079.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96080.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96081.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96085.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96086.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96087.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96089.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96090.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96093.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96095.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96096.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96097.1 is in your taxonomy file and is not in your template file. Please corre ct. Z96098.1 is in your taxonomy file and is not in your template file. Please corre ct. Z99997.1 is in your taxonomy file and is not in your template file. Please corre ct. Z99998.1 is in your taxonomy file and is not in your template file. Please corre ct. Z99999.1 is in your taxonomy file and is not in your template file. Please corre ct. DONE. It took 24 seconds get probabilities. such results came out 1. what is wrong with “Z99999.1 is in your taxonomy file and is not in your template file. Please corre ct.” 2)a picked “\*.taxonomy” output file was not found, therefore I could not continue to run “remove.lineage”. Is there anything wrong with my command?? or else ? Thanks for your advice ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [April 24, 2017, 12:50pm UTC](https://forum.mothur.org/t/problems-in-classify-seqs/3218/2 "2017-04-24T12:50:18Z")
You want reference=silva.bacteria.fasta not reference=silva.gold.ng.fasta