# error with filter.seqs or chimera.uchime???
**URL:** https://forum.mothur.org/t/error-with-filter-seqs-or-chimera-uchime/3154
**Category:** mothur bugs
**Created:** [March 8, 2017, 3:05am UTC](https://forum.mothur.org/t/error-with-filter-seqs-or-chimera-uchime/3154 "2017-03-08T03:05:59Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@sekhwal](https://forum.mothur.org/u/sekhwal)
#### Post date: [March 8, 2017, 3:05am UTC](https://forum.mothur.org/t/error-with-filter-seqs-or-chimera-uchime/3154/1 "2017-03-08T03:05:59Z")
Hi… i am trying to analysis my 18sRNA sequencing data. However, Mothur is quitting at chimera.uchime step. I am not getting sure where i am doing wrong. Some time filter.seqs showing “filtered alignment: 0”. However, I tried with change parameters such as trump=., or trump=T, vertical=T and now “getting filtered alignment: some numbers” but still further not able to run chimera.uchime step. Please have a look into below process and suggest. Thanks…
* * *
mothur \>
summary.seqs(fasta=stability.trim.contigs.fasta)
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 35 35 0 2 1
2.5%-tile: 1 389 389 0 4 28367
25%-tile: 1 418 418 0 5 283667
Median: 1 421 421 2 6 567334
75%-tile: 1 427 427 9 6 851000
97.5%-tile: 1 576 576 28 9 1106300
Maximum: 1 602 602 118 300 1134666
Mean: 1 429.957 429.957 5.77743 5.78735
# of Seqs: 1134666
Output File Names:
stability.trim.contigs.summary
It took 87 secs to summarize 1134666 sequences.
mothur \>
summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table, processors=2)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 13127 22553 403 0 5 8812
25%-tile: 13127 22553 418 0 5 88120
Median: 13127 22553 420 0 6 176239
75%-tile: 13127 22553 427 0 6 264358
97.5%-tile: 13127 22553 438 0 6 343665
Maximum: 43116 43116 576 0 15 352476
Mean: 13155.1 22517.4 418.227 0 5.67452
# of unique seqs: 115665
total # of seqs: 352476
Output File Names:
stability.trim.contigs.good.unique.summary
It took 460 secs to summarize 352476 sequences.
mothur \>
screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table, summary=stability.trim.contigs.good.unique.summary, start=13127, end=22553, maxhomop=8)
Using 2 processors.
Output File Names:
stability.trim.contigs.good.unique.good.summary
stability.trim.contigs.good.unique.good.align
stability.trim.contigs.good.unique.bad.accnos
stability.trim.contigs.good.good.count\_table
It took 799 secs to screen 115665 sequences.
mothur \>
filter.seqs(fasta=stability.trim.contigs.good.unique.align, vertical=T, trump=T)
Using 2 processors.
Creating Filter…
Running Filter…
Length of filtered alignment: 788
Number of columns removed: 49212
Length of the original alignment: 50000
Number of sequences used to construct filter: 115665
Output File Names:
stability.filter
stability.trim.contigs.good.unique.filter.fasta
mothur \>
pre.cluster(fasta=stability.trim.contigs.good.unique.filter.fasta, count=stability.trim.contigs.good.count\_table, diffs=0)
Using 2 processors.
Processing group JCT-28-2\_S24:
Processing group JCT-40-3\_S25:
14274 136 14138
Total number of sequences before pre.cluster was 14274.
pre.cluster removed 14138 sequences.
It took 1 secs to cluster 14274 sequences.
Processing group JCT-3-3\_S23:
5530 66 5464
Total number of sequences before pre.cluster was 5530.
pre.cluster removed 5464 sequences.
It took 1 secs to cluster 5530 sequences.
71318 433 70885
Total number of sequences before pre.cluster was 71318.
pre.cluster removed 70885 sequences.
It took 7 secs to cluster 71318 sequences.
Processing group JNT-32-4\_S20:
24951 208 24743
Total number of sequences before pre.cluster was 24951.
pre.cluster removed 24743 sequences.
It took 2 secs to cluster 24951 sequences.
Processing group SCT-3-3\_S35:
8377 115 8262
Total number of sequences before pre.cluster was 8377.
pre.cluster removed 8262 sequences.
It took 0 secs to cluster 8377 sequences.
It took 24 secs to run pre.cluster.
Output File Names:
stability.trim.contigs.good.unique.filter.precluster.fasta
stability.trim.contigs.good.unique.filter.precluster.count\_table
stability.trim.contigs.good.unique.filter.precluster.JCT-28-2\_S24.map
stability.trim.contigs.good.unique.filter.precluster.JCT-3-3\_S23.map
stability.trim.contigs.good.unique.filter.precluster.JCT-40-3\_S25.map
stability.trim.contigs.good.unique.filter.precluster.JNT-32-4\_S20.map
stability.trim.contigs.good.unique.filter.precluster.SCT-3-3\_S35.map
mothur \>
chimera.uchime(fasta=stability.trim.contigs.good.unique.filter.precluster.fasta, count=stability.trim.contigs.good.unique.filter.precluster.count\_table, dereplicate=t)
Using 2 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 stability.trim.contigs.good.unique.filter.precluster.fasta …
It took 3 secs to check 26 sequences from group JCT-40-3\_S25.
It took 0 secs to check 5 sequences from group JNT-32-4\_S20.
It took 0 secs to check 3 sequences from group SCT-3-3\_S35.
[ERROR]: stability.trim.contigs.good.unique.filter.precluster.denovo.uchime.chimerasJCT-28-2\_S24 is blank. Please correct.
It took 8 secs to check 136 sequences from group JCT-28-2\_S24.
[ERROR]: stability.trim.contigs.good.unique.filter.precluster.denovo.uchime.chimerasJCT-3-3\_S23 is blank. Please correct.
It took 3 secs to check 66 sequences from group JCT-3-3\_S23.
Output File Names:
stability.trim.contigs.good.unique.filter.precluster.denovo.uchime.pick.count\_table
stability.trim.contigs.good.unique.filter.precluster.denovo.uchime.chimeras
stability.trim.contigs.good.unique.filter.precluster.denovo.uchime.accnos
mothur \> chimera.uchime(fasta=stability.trim.contigs.good.unique.filter.precluster.fasta, reference=silva.seed\_v123.align, dereplicate=t)
Using 2 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 stability.trim.contigs.good.unique.filter.precluster.fasta …
[ERROR]: process 1 only processed 0 of 0 sequences assigned to it, quitting.
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [March 10, 2017, 1:48pm UTC](https://forum.mothur.org/t/error-with-filter-seqs-or-chimera-uchime/3154/2 "2017-03-10T13:48:45Z")
What happens when you run screen.seqs(fasta=stability.trim.contigs.good.unique.good.align)?
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### Author:  [@sekhwal](https://forum.mothur.org/u/sekhwal)
#### Post date: [March 10, 2017, 7:28pm UTC](https://forum.mothur.org/t/error-with-filter-seqs-or-chimera-uchime/3154/3 "2017-03-10T19:28:30Z")
Hi, Here is output of screen.seqs(fasta=stability.trim.contigs.good.unique.align)? However, i am not getting to run chimera.uchime. Usually it shows
“…short sequences (–minlen 10, shortest 0) discarded from stability.trim.contigs.good.unique.filter.precluster.temp”.
Thanks
* * *
mothur \> screen.seqs(fasta=stability.trim.contigs.good.unique.align)
Using 1 processors.
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Output File Names:
stability.trim.contigs.good.unique.good.align
stability.trim.contigs.good.unique.bad.accnos
It took 106 secs to screen 27049 sequences.
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [March 13, 2017, 1:13pm UTC](https://forum.mothur.org/t/error-with-filter-seqs-or-chimera-uchime/3154/4 "2017-03-13T13:13:51Z")
Sorry, I meant to ask what the output of summary.seqs was after running screen.seqs
Pat