I am trying to use the pre.cluster command but I keep getting this error. I am not sure what it means or how to fix it.
mothur > pre.cluster(fasta=SRR830919.unique.fasta, count=SRR830919.good.count_table, diffs=2)
Unable to open SRR830919.unique.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta.
Unable to open SRR830919.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.good.count_table.
Using 8 processors.
[ERROR]: 'SRR830919.37041.2' is not in your name or count file, please correct.
When using running without group information mothur can only use 1 processor, continuing.
Code done prior:
Last login: Wed Aug 3 23:40:52 on ttys000
meghanstern@MacBook-Pro ~ % /Users/meghanstern/Desktop/mothur/mothur ; exit;
Mac version
Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
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
For questions and analysis support, please visit our forum at https://forum.mothur.org
Type 'quit()' to exit program
[NOTE]: Setting random seed to 19760620.
Interactive Mode
mothur > unique.seqs(fasta=SRR830919.fasta)
Unable to open SRR830919.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.fasta.
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Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta
/Users/meghanstern/Desktop/mothur/SRR830919.count_table
mothur > summary.seqs(count=SRR830919.count_table)
Using /Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta as input file for the fasta parameter.
Unable to open SRR830919.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.count_table.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 56 56 0 1 1
2.5%-tile: 1 371 371 0 4 6427
25%-tile: 1 484 484 0 5 64261
Median: 1 538 538 2 5 128522
75%-tile: 1 582 582 4 6 192783
97.5%-tile: 1 745 745 18 15 250617
Maximum: 1 1196 1196 92 90 257043
Mean: 1 538 538 3 5
# of unique seqs: 256205
total # of seqs: 257043
It took 4 secs to summarize 257043 sequences.
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.unique.summary
mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdotsF)
Unable to open silva.bacteria.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/silva.bacteria.fasta.
Using 8 processors.
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[NOTE]: no sequences were bad, removing /Users/meghanstern/Desktop/mothur/silva.bacteria.bad.accnos
It took 6 secs to screen 14956 sequences.
Output File Names:
/Users/meghanstern/Desktop/mothur/silva.bacteria.pcr.fasta
mothur > rename.file(input=silva.bacteria.pcr.fasta, new=silva.v4.fasta)
Unable to open silva.bacteria.pcr.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/silva.bacteria.pcr.fasta.
Current files saved by mothur:
fasta=/Users/meghanstern/Desktop/mothur/silva.bacteria.pcr.fasta
count=/Users/meghanstern/Desktop/mothur/SRR830919.count_table
processors=8
summary=/Users/meghanstern/Desktop/mothur/SRR830919.unique.summary
mothur > summary.seqs(fasta=silva.v4.fasta)
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 13424 269 0 3 1
2.5%-tile: 1 13424 291 0 4 374
25%-tile: 1 13424 292 0 4 3740
Median: 1 13424 292 0 4 7479
75%-tile: 1 13424 292 0 5 11218
97.5%-tile: 1 13424 293 1 6 14583
Maximum: 3 13424 350 5 9 14956
Mean: 1 13424 291 0 4
# of Seqs: 14956
It took 2 secs to summarize 14956 sequences.
Output File Names:
silva.v4.summary
mothur > align.seqs(fasta=SRR830919.unique.fasta, reference=silva.v4.fasta)
Unable to open SRR830919.unique.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta.
Using 8 processors.
Reading in the silva.v4.fasta template sequences... DONE.
It took 3 to read 14956 sequences.
Aligning sequences from /Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta ...
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It took 173 secs to align 256205 sequences.
[WARNING]: 239375 of your sequences generated alignments that eliminated too many bases, a list is provided in /Users/meghanstern/Desktop/mothur/SRR830919.unique.flip.accnos.
[NOTE]: 78119 of your sequences were reversed to produce a better alignment.
It took 173 seconds to align 256205 sequences.
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.unique.align
/Users/meghanstern/Desktop/mothur/SRR830919.unique.align_report
/Users/meghanstern/Desktop/mothur/SRR830919.unique.flip.accnos
mothur > summary.seqs(fasta=SRR830918.unique.align, count=SRR830918.count_tabl)
mothur > summary.seqs(fasta=SRR830919.unque.align, count=SRR830919.count_table)
Unable to open SRR83099.unique.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR83099.unique.align.
Unable to open /Users/meghanstern/Desktop/mothur/SRR83099.unique.align. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR83099.unique.align.
Unable to open /Users/meghanstern/Desktop/mothur/SRR83099.unique.align.
Unable to open SRR83099.unique.align
Unable to open SRR830198.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830198.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830198.count_table. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830198.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830198.count_table.
Unable to open SRR830198.count_table
Using 8 processors.
[ERROR]: did not complete summary.seqs.
mothur > summary.seqs(fasta=SRR830919.unique.align, count=SRR83019.count_table)
Unable to open SRR830919.unique.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.align.
Unable to open SRR83019.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR83019.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR83019.count_table. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR83019.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR83019.count_table.
Unable to open SRR83019.count_table
Using 8 processors.
[ERROR]: did not complete summary.seqs.
mothur > summary.seqs(fasta=SRR830919.unique.align, count=SRR830919.count_table)
Unable to open SRR830919.unique.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.align.
Unable to open SRR830919.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.count_table.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 1 1236 6 0 1 6427
25%-tile: 1 13424 9 0 1 64261
Median: 12065 13424 13 0 2 128522
75%-tile: 13393 13424 114 0 4 192783
97.5%-tile: 13399 13424 299 2 5 250617
Maximum: 13424 13424 343 62 61 257043
Mean: 7844 11341 74 0 2
# of unique seqs: 256205
total # of seqs: 257043
It took 25 secs to summarize 257043 sequences.
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.unique.summary
mothur > screen.seqs(fasta=SRR830918.unique.align, count=SRR830918.count_table, start=5056, end=13424)
Unable to open SRR830918.unique.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830918.unique.align.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.unique.align. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830918.unique.align.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.unique.align.
Unable to open SRR830918.unique.align
Unable to open SRR830918.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830918.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.count_table. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830918.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.count_table.
Unable to open SRR830918.count_table
Using 8 processors.
[ERROR]: did not complete screen.seqs.
mothur > screen.seqs(fasta=SRR830919.unique.align, count=SRR830919.count_table, start=5056, end=13424)
Unable to open SRR830919.unique.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.align.
Unable to open SRR830919.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.count_table.
Using 8 processors.
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It took 18 secs to screen 256205 sequences, removed 213843.
/******************************************/
Running command: remove.seqs(accnos=/Users/meghanstern/Desktop/mothur/SRR830919.unique.bad.accnos.temp, count=/Users/meghanstern/Desktop/mothur/SRR830919.count_table)
Removed 214518 sequences from /Users/meghanstern/Desktop/mothur/SRR830919.count_table.
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.pick.count_table
/******************************************/
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.unique.good.align
/Users/meghanstern/Desktop/mothur/SRR830919.unique.bad.accnos
/Users/meghanstern/Desktop/mothur/SRR830919.good.count_table
It took 20 secs to screen 256205 sequences.
mothur > summary.seqs(fasta=SRR830918.unique.good.align, count=SRR830918.good.count_table)
mothur > 98.good.count_table)
Unable to open SRR830918.unique.good.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830918.unique.good.align.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.unique.good.align. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830918.unique.good.align.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.unique.good.align.
Unable to open SRR830918.unique.good.align
Unable to open SRR830998.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830998.good.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830998.good.count_table. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830998.good.count_table.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830998.good.count_table.
Unable to open SRR830998.good.count_table
Using 8 processors.
[ERROR]: did not complete summary.seqs.
mothur > summary.seqs(fasta=SRR830919.unique.good.align, count=SRR830919.good.count_table)
Unable to open SRR830919.unique.good.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.align.
Unable to open SRR830919.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.good.count_table.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 13424 150 0 3 1
2.5%-tile: 1 13424 181 0 3 1064
25%-tile: 1 13424 290 0 4 10632
Median: 1 13424 292 0 4 21263
75%-tile: 1 13424 295 0 5 31894
97.5%-tile: 4399 13424 310 4 6 41462
Maximum: 4535 13424 343 62 61 42525
Mean: 655 13424 282 0 4
# of unique seqs: 42362
total # of seqs: 42525
It took 4 secs to summarize 42525 sequences.
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.unique.good.summary
mothur > filter.seqs(fasta=SRR830919.unique.good.align, vertical=T, trump=.)
Unable to open SRR830919.unique.good.align. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.align.
Using 8 processors.
Creating Filter...
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It took 4 secs to create filter for 42362 sequences.
Running Filter...
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It took 2 secs to filter 42362 sequences.
Length of filtered alignment: 383
Number of columns removed: 13041
Length of the original alignment: 13424
Number of sequences used to construct filter: 42362
Output File Names:
/Users/meghanstern/Desktop/mothur/SRR830919.filter
/Users/meghanstern/Desktop/mothur/SRR830919.unique.good.filter.fasta
mothur > unique.seqs(fasta=SRR830919.unique.good.fasta, count=SRR830919.good.count_table)
Unable to open SRR830919.unique.good.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta.
Unable to open SRR830919.unique.good.fasta
Unable to open SRR830919.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.good.count_table.
[ERROR]: did not complete unique.seqs.
mothur > pre.cluster(fasta=SRR830919.unique.good.fasta, count=SRR830919.good.count_table, diffs=2)
Unable to open SRR830919.unique.good.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830919.unique.good.fasta.
Unable to open SRR830919.unique.good.fasta
Unable to open SRR830919.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.good.count_table.
Using 8 processors.
[ERROR]: did not complete pre.cluster.
mothur > pre.cluster(fasta=SRR830919.unique.fasta, count=SRR830919.good.count_table, diffs=2)
Unable to open SRR830919.unique.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta.
Unable to open SRR830919.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.good.count_table.
Using 8 processors.
[ERROR]: 'SRR830919.37041.2' is not in your name or count file, please correct.
When using running without group information mothur can only use 1 processor, continuing.
mothur > pre.cluster(fasta=SRR830919.unique.fasta, count=SRR830919.good.count_table, diffs=2)
Unable to open SRR830919.unique.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.unique.fasta.
Unable to open SRR830919.good.count_table. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830919.good.count_table.
Using 8 processors.
[ERROR]: 'SRR830919.37041.2' is not in your name or count file, please correct.
When using running without group information mothur can only use 1 processor, continuing.