# Align.seqs issue **URL:** \ **Category:** Commands in mothur\ **Created:** [December 22, 2017, 1:11am UTC](https://forum.mothur.org/t/align-seqs-issue/3468 "2017-12-22T01:11:18Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![amwalkero0o](https://avatars.discourse-cdn.com/v4/letter/a/839c29/32.png) [@amwalkero0o](https://forum.mothur.org/u/amwalkero0o)\ **Post date:** [December 22, 2017, 1:11am UTC](https://forum.mothur.org/t/align-seqs-issue/3468/1 "2017-12-22T01:11:18Z")
Hello, I wanted to see what would change w.r.t. to my data if I aligned my seqs with the full mothur formatted Silva 132 align file. So I created the align file using the instructions here: [http://blog.mothur.org/2017/03/22/SILVA-v128-reference-files/](http://blog.mothur.org/2017/03/22/SILVA-v128-reference-files/) I ended up using only the degap and unique seqs commands, not screen or pcr seqs, so as not to get rid of any sequences. Since I am running the align seqs on a high compute cluster, I figured I’d give it a go. Everything looked like it worked fine, but I got the following 5 errors returned with my logfile. [ERROR]: BA\_undil\_data.trim.contigs.good.unique.align93169.num.temp is blank. Please correct. [ERROR]: BA\_undil\_data.trim.contigs.good.unique.align93175.num.temp is blank. Please correct. [ERROR]: BA\_undil\_data.trim.contigs.good.unique.align93182.num.temp is blank. Please correct. [ERROR]: BA\_undil\_data.trim.contigs.good.unique.align93192.num.temp is blank. Please correct. [ERROR]: BA\_undil\_data.trim.contigs.good.unique.align93193.num.temp is blank. Please correct. count.seqs and summary following alignment look good relative to my other mothur runs. What does this error mean and is there a way to understand graphically how well an alignment went, i.e. another way than looking at the individual lines of the report? My align.seqs code: mothur “#align.seqs(fasta=BA\_undil\_data.trim.contigs.good.unique.fasta, reference=silva.nrfull\_v132.align flip=T, processors=24)” Thank you and Happy Holidays! ---
**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:** [December 22, 2017, 3:01pm UTC](https://forum.mothur.org/t/align-seqs-issue/3468/2 "2017-12-22T15:01:55Z")
Hmmmm. Not sure - can you try using 1 processor and see if you get the error message? ---
**Author:** ![amwalkero0o](https://avatars.discourse-cdn.com/v4/letter/a/839c29/32.png) [@amwalkero0o](https://forum.mothur.org/u/amwalkero0o)\ **Post date:** [December 22, 2017, 8:15pm UTC](https://forum.mothur.org/t/align-seqs-issue/3468/3 "2017-12-22T20:15:40Z")
Sure, I will run it on our “big memory” cluster and let you know the outcome. ---
**Author:** ![amwalkero0o](https://avatars.discourse-cdn.com/v4/letter/a/839c29/32.png) [@amwalkero0o](https://forum.mothur.org/u/amwalkero0o)\ **Post date:** [December 30, 2017, 8:48pm UTC](https://forum.mothur.org/t/align-seqs-issue/3468/4 "2017-12-30T20:48:52Z")
That worked, thanks!