# Mismatch in align and tax file? **URL:** \ **Category:** mothur bugs\ **Created:** [November 29, 2021, 8:07pm UTC](https://forum.mothur.org/t/mismatch-in-align-and-tax-file/21198 "2021-11-29T20:07:38Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![samche42](https://avatars.discourse-cdn.com/v4/letter/s/ccd318/32.png) [@samche42](https://forum.mothur.org/u/samche42)\ **Post date:** [November 29, 2021, 8:07pm UTC](https://forum.mothur.org/t/mismatch-in-align-and-tax-file/21198/1 "2021-11-29T20:07:38Z")
Hi! I recently tried running mothur on CyVerse (Ubuntu command line). I downloaded both mothur (and all its buddy tools) as well as the silva database directly to the site using wget. I.e.: ```auto wget https://github.com/mothur/mothur/releases/download/v1.46.1/Mothur.Ubuntu_20.zip unzip Mothur.Ubuntu_20.zip rm Mothur.Ubuntu_20.zip mv mothur/ Mothur/ mv Mothur/* ./ ``` #Get databases `wget https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v138_1.tgz` #Uncompress database file `tar xzvf silva.nr_v138_1.tgz` #Start mother `./mothur` Everything runs hunky-dory until I get to the classify step, where I try and classify the reads using teh unaltered, untouched silva files: #Next we need to identify the seqs `classify.seqs(fasta=ABC.trim.contigs.good.unique.pick.fasta, count=ABC.trim.contigs.good.pick.count_table,reference=silva.nr_v138_1.align, taxonomy=silva.nr_v138_1.tax, cutoff=80)` This resulted in several iterations of " ‘XXX’ is in your template file and is not in your taxonomy file. Please correct." I rootled around online and found some people had had a similar issue and tried the following work around that had been suggested [18S Analysis: Trimmed align file used in classify.seqs is missing taxons · Issue #505 · mothur/mothur · GitHub](https://github.com/mothur/mothur/issues/505) : #Fix the broken databases ```auto list.seqs(fasta=silva.nr_v138_1.align) get.seqs(taxonomy=silva.nr_v138_1.tax, accnos=silva.nr_v138_1.accnos) ``` I also looked for any naughty spaces that may be in the tax file, as suggested by Dr. Schloss in this post [classify.seqs errors in reading taxonomy file](https://forum.mothur.org/t/classify-seqs-errors-in-reading-taxonomy-file/1855). However, upon running the classify.seqs step after that (with my newly made silva.nr\_v138\_1.pick.tax file), I had the same error that may have actually had more “missing” taxa. The most puzzling part is, is that I ran this exact set of sequences through mothur (with the same 138 silva release) on both my Mac and on one of our Linux servers without issue. I similarly tried using the databases (tax and align) that I had downloaded to each of those in the Cyverse environment, and alas, the same error. I’m very flummoxed. Any help on getting this working would be really appreciated! 🙂 Sam ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [November 30, 2021, 9:02pm UTC](https://forum.mothur.org/t/mismatch-in-align-and-tax-file/21198/2 "2021-11-30T21:02:36Z")
I use the terminal app to run mothur, not CyVerse. I am not able to reproduce this issue on our Ubuntu test machines with terminal. ---
**Author:** ![samche42](https://avatars.discourse-cdn.com/v4/letter/s/ccd318/32.png) [@samche42](https://forum.mothur.org/u/samche42)\ **Post date:** [December 7, 2021, 9:51pm UTC](https://forum.mothur.org/t/mismatch-in-align-and-tax-file/21198/3 "2021-12-07T21:51:41Z")
Oki dokes! Ya, I couldn’t reproduce it in terminal either. I’ll bug the CyVerse admin and see if they know what the problem is 🙂 Thanks all the same! ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [December 17, 2021, 9:52pm UTC](https://forum.mothur.org/t/mismatch-in-align-and-tax-file/21198/4 "2021-12-17T21:52:16Z")
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