# align seqs
**URL:** https://forum.mothur.org/t/align-seqs/1492
**Category:** Commands in mothur
**Created:** [September 6, 2013, 6:21pm UTC](https://forum.mothur.org/t/align-seqs/1492 "2013-09-06T18:21:07Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@marniehall](https://forum.mothur.org/u/marniehall)
#### Post date: [September 6, 2013, 6:21pm UTC](https://forum.mothur.org/t/align-seqs/1492/1 "2013-09-06T18:21:07Z")
I am new to Mothur and trying to run the example data set on a PC windows 7. When I use the command “align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)” I only get two out of the three outputs…
Output File Names:
stability.trim.contigs.good.unique.align
stability.trim.contigs.good.unique.align.report
stability.trim.contigs.good.unique.flip.accnos
I do not get the flip.accnos file. Any idea why?
Thanks,
Marnie
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [September 6, 2013, 8:39pm UTC](https://forum.mothur.org/t/align-seqs/1492/2 "2013-09-06T20:39:51Z")
It’s probably empty and not actually created.
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### Author:  [@marniehall](https://forum.mothur.org/u/marniehall)
#### Post date: [September 11, 2013, 1:49pm UTC](https://forum.mothur.org/t/align-seqs/1492/3 "2013-09-11T13:49:14Z")
So what command do I use to create it?
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [September 11, 2013, 5:27pm UTC](https://forum.mothur.org/t/align-seqs/1492/4 "2013-09-11T17:27:44Z")
You would only get that file if it thought flipping some of the sequences would help the alignment. Since the file is empty there was no need to flip any of them.
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### Author:  [@marniehall](https://forum.mothur.org/u/marniehall)
#### Post date: [September 23, 2013, 4:21pm UTC](https://forum.mothur.org/t/align-seqs/1492/5 "2013-09-23T16:21:29Z")
I still can’t get past the accnos file. Here is what the log file is saying:
Output File Names:
MarnieSta.contigs.good.count.summary
mothur \> align.seqs(fasta=MarnieSta.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)
Using 1 processors.
Reading in the silva.v4.fasta template sequences… DONE.
It took 65 to read 14956 sequences.
Aligning sequences from MarnieSta.trim.contigs.good.unique.fasta …
It took 8315 secs to align 568960 sequences.
Output File Names:
MarnieSta.trim.contigs.good.unique.align
MarnieSta.trim.contigs.good.unique.align.report
mothur \> remove.seqs(fasta=MarnieSta.trim.contigs.good.unique.align, name=MarnieSta.trim.contigs.good.names, group=MarnieSta.contigs.good.groups)
You have no valid accnos file and accnos is required.
[ERROR]: did not complete remove.seqs.
What do I write in the command line to get it to remove seqs? If i try to skip this step it tells me that I don't have an accnos file. My SOP is slightly different from yours so is that the problem? I will list the next few commands so you can see if they are right. I can't get past this step. I have tried to take out the flip.acnos command but it doesn't help.
1. mothur \> remove.seqs(fasta=MarnieSta.trim.contigs.good.unique.align, name=MarnieSta.trim.contigs.good.names, group=MarnieSta.contigs.good.groups, accnos=MarnieSta.trim.contigs.good.unique.flip.accnos)
Removed 8 sequences from your name file.
Removed 8 sequences from your fasta file.
Removed 8 sequences from your group file.
Output File Names:
MarnieSta.trim.contigs.good.pick.names
MarnieSta.trim.contigs.good.unique.pick.align
MarnieSta.contigs.good.pick.groups
10) mothur \> count.seqs(name=MarnieSta.trim.contigs.good.pick.names, group=MarnieSta.contigs.good.pick.groups)
Total number of sequences: 351814
Output File Names:
MarnieSta.trim.contigs.good.pick.count\_table
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [September 23, 2013, 6:05pm UTC](https://forum.mothur.org/t/align-seqs/1492/6 "2013-09-23T18:05:44Z")
Sorry - but I’m not clear what you’re doing or what’s going wrong…
In the first align.seqs you posted there wasn’t a flip.accnos file created (from the output you sent, at least). And yes, remove.seqs requires an accnos file - those are the sequences that get removed.