HELP Pre.Cluster Not Working

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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257043	256205

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.

You count file has a good in it while your fasta doesn’t. It looks like you might be using the wrong fasta file.

Pat

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