I’m getting a mysterious error when I use chimera.slayer:
“sequence.in.fasta.file is not the same length as the template sequences. Aborting!”
In two out of five fasta files that I’m trying to run I get this error on the first sequence. I can’t find any difference between sequences that would account for this error. In all five fasta files the length of the first sequence is around 250 bp. Template files and batch files are identical between runs. I’ve pasted the log file below. If anyone has any suggestions I’d appreciate it!
Windows version
Using ReadLine
mothur v.1.11.0
Last updated: 6/18/2010
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
Distributed under the GNU General Public License
Type ‘help()’ for information on the commands that are available
Type ‘quit()’ to exit program
Batch Mode
mothur > unique.seqs(fasta=15S.fna)
Output File Names:
15S.unique.fna
15S.names
mothur > align.seqs(candidate=15S.unique.fna, template=core_set_aligned.imputed.fasta, ksize=8, align=needleman, gapopen=-2)
Reading in the core_set_aligned.imputed.fasta template sequences… DONE.
Aligning sequences from 15S.unique.fna …
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It took 72 secs to align 4717 sequences.
Output File Names: 15S.unique.align 15S.unique.align.report
mothur > screen.seqs(start=1903, fasta=15S.unique.align, minlength=100, maxambig=0, group=15S.groups, name=15S.names)
Output File Names:
15S.unique.good.align
15S.unique.bad.align
15S.unique.bad.accnos
15S.good.names
15S.bad.names
15S.good.groups
15S.bad.groups
It took 10 secs to screen 4717 sequences.
mothur > filter.seqs(fasta=15S.unique.good.align, vertical=T, trump=.)
Creating Filter…
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Running Filter...
Length of filtered alignment: 264 Number of columns removed: 7418 Length of the original alignment: 7682 Number of sequences used to construct filter: 4632
Output File Names:
15S.filter
15S.unique.good.filter.fasta
mothur > unique.seqs(fasta=15S.unique.good.filter.fasta)
Output File Names:
15S.unique.good.filter.unique.fasta
15S.unique.good.filter.names
mothur > pre.cluster(fasta=15S.unique.good.filter.unique.fasta, name=15S.unique.good.filter.names) Total number of sequences before precluster was 1587. pre.cluster removed 481 sequences.
Output File Names:
15S.unique.good.filter.unique.precluster.fasta
15S.unique.good.filter.unique.precluster.names
mothur > filter.seqs(fasta=core_set_aligned.imputed.fasta, vertical=T, trump=.) Creating Filter... 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000 2100 2200 2300 2400 2500 2600 2700 2800 2900 3000 3100 3200 3300 3400 3500 3600 3700 3800 3900 4000 4100 4200 4300 4400 4500 4600 4700 4800 4900 4938
Running Filter...
Length of filtered alignment: 3373 Number of columns removed: 4309 Length of the original alignment: 7682 Number of sequences used to construct filter: 4938
Output File Names:
core_set_aligned.filter
core_set_aligned.imputed.filter.fasta
mothur > chimera.slayer(fasta=15S.unique.good.filter.unique.precluster.fasta, template=core_set_aligned.imputed.filter.fasta, minsnp=100) Reading sequences from core_set_aligned.imputed.filter.fasta...Done. Reading sequences from 15S.unique.good.filter.unique.precluster.fasta...Done.