# align.seqs issue/ groups removal
**URL:** https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304
**Category:** mothur bugs
**Created:** [March 17, 2015, 4:56pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304 "2015-03-17T16:56:05Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@sid87](https://forum.mothur.org/u/sid87)
#### Post date: [March 17, 2015, 4:56pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304/1 "2015-03-17T16:56:05Z")
please find summary results i have the number of seqs are in single digit is it normal?
also some of my groups have been completely removed again no clue why
mothur \> summary.seqs(fasta=s3rfc.trim.contigs.good.unique.fasta, count=s3rfc.trim.contigs.good.count\_table)
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 265 265 0 4 1
2.5%-tile: 1 0 0 0 4 1
25%-tile: 1 268 268 0 4 2
Median: 1 268 268 0 5 3
75%-tile: 1 268 268 0 5 4
97.5%-tile: 1 268 268 0 5 5
Maximum: 1 268 268 0 5 5
Mean: 1 267.4 267.4 0 4.6
# of unique seqs: 5
total # of seqs: 5
Output File Names:
s3rfc.trim.contigs.good.unique.summary
mothur \> align.seqs(fasta=s3rfc.trim.contigs.good.unique.fasta, reference=silva.v5.fasta)
Using 1 processors.
Reading in the silva.v5.fasta template sequences… DONE.
It took 7 to read 14956 sequences.
Aligning sequences from s3rfc.trim.contigs.good.unique.fasta …
5
Some of you sequences generated alignments that eliminated too many bases, a list is provided in s3rfc.trim.contigs.good.unique.flip.accnos. If you set the flip parameter o true mothur will try aligning the reverse compliment as well.
It took 0 secs to align 5 sequences.
mothur \> align.seqs(fasta=s3rfc.trim.contigs.good.unique.fasta, reference=silva.v5.fasta, flip=t, processors=8)
Using 8 processors.
Reading in the silva.v5.fasta template sequences… DONE.
It took 7 to read 14956 sequences.
Aligning sequences from s3rfc.trim.contigs.good.unique.fasta …
1
1
1
1
1
Some of you sequences generated alignments that eliminated too many bases, a list is provided in s3rfc.trim.contigs.good.unique.flip.accnos. If the reverse compliment provd to be better it was reported.
It took 0 secs to align 5 sequences.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 4466 129 0 4 1
2.5%-tile: 1 4466 129 0 4 1
25%-tile: 1 4466 129 0 4 2
Median: 1 4519 129 0 4 3
75%-tile: 1239 11550 265 0 5 4
97.5%-tile: 1241 12064 268 0 5 5
Maximum: 1241 12064 268 0 5 5
Mean: 496.6 7413 184 0 4.4
# of unique seqs: 5
total # of seqs: 5
mothur \> screen.seqs(fasta=s3rfc.trim.contigs.good.unique.align, count=s3rfc.trim.contigs.good.count\_table, summary=s3rfc.trim.contigs.good.unique.summary, start=1241, end=12064, maxhomop=8)
Using 1 processors.
Processing sequence: 5
Removing group: S3RFCBJ3 because all sequences have been removed.
Removing group: S3RFCBJ6 because all sequences have been removed.
I am sorry i am newbie (and excuse if some one has already posted the solution for such problem earlier could not find it)
thanks
sid
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 18, 2015, 12:56pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304/2 "2015-03-18T12:56:17Z")
It looks like most of your sequences were removed before these commands. Possibly in a screen.seqs command? Could you post the commands you ran before these?
---
### Author:  [@sid87](https://forum.mothur.org/u/sid87)
#### Post date: [March 18, 2015, 1:53pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304/3 "2015-03-18T13:53:06Z")
hi,
I figured out the reason for my earlier problem, no of bases were the problem…however i ran in to a new problem which i have not face before.
This time its with the chimera.uchime command, please find below
mothur \> chimera.uchime(fasta=brfc.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=brfc.trim.contigs.good.unique.good.filter.unique.precluster.count\_table, dereplicate=t)
Using 1 processors.
uchime by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
Checking sequences from brfc.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 75 sequences
00:00 1.9Mb 100.0% 0/74 chimeras found (0.0%)
It took 0 secs to check 75 sequences from group BRFCBA3.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 47 sequences
00:00 1.9Mb 100.0% 0/46 chimeras found (0.0%)
It took 0 secs to check 47 sequences from group BRFCBA4.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 88 sequences
00:00 1.8Mb 100.0% 0/87 chimeras found (0.0%)
It took 0 secs to check 88 sequences from group BRFCU1.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 115 sequences
00:00 1.8Mb 100.0% 0/114 chimeras found (0.0%)
It took 0 secs to check 115 sequences from group BRFCU2.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 110 sequences
00:00 1.8Mb 100.0% 0/109 chimeras found (0.0%)
It took 0 secs to check 110 sequences from group BRFCU6.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 114 sequences
00:00 1.8Mb 100.0% 0/113 chimeras found (0.0%)
It took 0 secs to check 114 sequences from group BRFCU7.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 120 sequences
00:00 1.8Mb 100.0% 0/119 chimeras found (0.0%)
It took 0 secs to check 120 sequences from group BRFCX2.
uchime v4.2.40
by Robert C. Edgar
[http://drive5.com/uchime](http://drive5.com/uchime)
This code is donated to the public domain.
00:00 18Mb 0.1% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
WARNING: Ignoring gaps in FASTA file ‘brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp’
00:00 18Mb 100.0% Reading brfc.trim.contigs.good.unique.good.filter.unique.precluster.temp
00:00 18Mb 123 sequences
00:00 1.8Mb 100.0% 0/122 chimeras found (0.0%)
It took 0 secs to check 123 sequences from group BRFCX3.
[ERROR]: brfc.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos is blank. Please correct.
Output File Names:
brfc.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count\_table
brfc.trim.contigs.good.unique.good.filter.unique.precluster.uchime.chimeras
brfc.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos
How can it be blank? when i set dereplicate=F the following is the result
It took 0 secs to check 123 sequences from group BRFCX3.
It took 1 secs to check 792 sequences. 0 chimeras were found.
The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples.
Output File Names:
brfc.trim.contigs.good.unique.good.filter.unique.precluster.uchime.chimeras
brfc.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos
Best,
Sid
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 18, 2015, 1:59pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304/4 "2015-03-18T13:59:39Z")
Uchime is reporting 0 chimeras across all your groups.
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### Author:  [@sid87](https://forum.mothur.org/u/sid87)
#### Post date: [March 18, 2015, 2:19pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304/5 "2015-03-18T14:19:28Z")
yes true but how do i proceed with the pipeline, the next command is remove.seqs which I am unable to run as accnos is blank !
should i directly run classify.seqs?
Thanks.
Best,
Sid
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 19, 2015, 1:17pm UTC](https://forum.mothur.org/t/align-seqs-issue-groups-removal/2304/6 "2015-03-19T13:17:03Z")
You do not need to run the remove.seqs command because there are no chimeras to remove. You can proceed with the pipeline.