# Silva reference files bug

**URL:** <https://forum.mothur.org/t/silva-reference-files-bug/2209>\
**Category:** mothur bugs\
**Created:** [January 20, 2015, 12:55pm UTC](https://forum.mothur.org/t/silva-reference-files-bug/2209 "2015-01-20T12:55:33Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![peleliu](https://avatars.discourse-cdn.com/v4/letter/p/8e7dd6/32.png) [@peleliu](https://forum.mothur.org/u/peleliu)\
**Post date:** [January 20, 2015, 12:55pm UTC](https://forum.mothur.org/t/silva-reference-files-bug/2209/1 "2015-01-20T12:55:33Z")

</div>

Hi,  
My Mothur is unable to read the silva reference files in align.seqs, please help…

## using Mothur 1.34.4 in Amazon EC2 linux server, I get the following results:

mothur\> align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.seed\_v119.align, flip=T, processors=4)  
using 4 processors.  
Reading in the silva.seed\_v119.align template sequences… [ERROR]: template is not aligned, aborting.  
DONE.  
It took 14 to read 10281 sequences.

## mothur\> align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.nr\_v119.align, flip=T, processors=4) using 4 processors. Reading in the silva.nr\_v119.align template sequences… Killed

I was thinking as a last resort to try using an older version of Mothur, but these are not compiled and I don’t know enough about compiling.

Thanks for your help,  
P.

---

<div class="post-metadata">

**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:** [January 21, 2015, 2:27pm UTC](https://forum.mothur.org/t/silva-reference-files-bug/2209/2 "2015-01-21T14:27:18Z")

</div>

Please only post your questions one one thread - we’ll follow up on your other thread.