mothur

Group is not a valid parameter

Hello Mothur Community

How to I work around the group is not a valid parameter message
I ran the following commands to get the initial group folder.

Linux version

Using ReadLine
mothur v.1.42.1
Last updated: 12/06/2021
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan

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 > fastq.info(fastq=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.fastq)
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Output File Names:
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.fasta
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.qual

mothur > summary.seqs(fasta=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.fasta, processors=8)

Using 8 processors.

	Start	End	NBases	Ambigs	Polymer	NumSeqs

Minimum: 1 25 25 0 1 1
2.5%-tile: 1 110 110 0 3 198700
25%-tile: 1 300 300 0 4 1986996
Median: 1 302 302 0 5 3973991
75%-tile: 1 303 303 0 5 5960986
97.5%-tile: 1 305 305 0 6 7749282
Maximum: 1 575 575 0 23 7947981
Mean: 1 288 288 0 4

of Seqs: 7947981

It took 32 secs to summarize 7947981 sequences.

Output File Names:
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.summary

mothur > trim.seqs(fasta=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.fasta, oligos=CXMicroMothurOligos.txt, maxambig=0, maxhomop=6, bdiffs=0, pdiffs=0, minlength=265, keepfirst=310, flip=F, processors=8)

Using 8 processors.
It took 100 secs to trim 7947981 sequences.

Group count:
BC1.515F 13
BC10.515F 3
BC11.515F 8
BC12.515F 13
BC13.515F 16
BC14.515F 9
BC15.515F 2
BC16.515F 7
BC17.515F 9
BC18.515F 6
BC19.515F 7
BC2.515F 3
BC20.515F 12
BC21.515F 11
BC22.515F 2
BC23.515F 7
BC24.515F 5
BC25.515F 2
BC26.515F 17
BC27.515F 15
BC28.515F 4
BC29.515F 16
BC3.515F 5
BC30.515F 2
BC31.515F 3
BC33.515F 1
BC34.515F 6
BC35.515F 2
BC36.515F 5
BC37.515F 11
BC38.515F 17
BC39.515F 5
BC4.515F 12
BC40.515F 2
BC41.515F 10
BC42.515F 2
BC43.515F 3
BC44.515F 3
BC45.515F 5
BC46.515F 16
BC47.515F 14
BC5.515F 3
BC6.515F 3
BC7.515F 3
BC8.515F 2
BC9.515F 11
Total of all groups is 333

Output File Names:
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.fasta
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.scrap.fasta
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.groups

mothur > summary.seqs(fasta=current, processors=8)
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.fasta as input file for the fasta parameter.

Using 8 processors.

	Start	End	NBases	Ambigs	Polymer	NumSeqs

Minimum: 1 265 265 0 3 1
2.5%-tile: 1 265 265 0 4 9
25%-tile: 1 265 265 0 5 84
Median: 1 266 266 0 5 167
75%-tile: 1 268 268 0 5 250
97.5%-tile: 1 275 275 0 6 325
Maximum: 1 291 291 0 6 333
Mean: 1 267 267 0 4

of Seqs: 333

It took 0 secs to summarize 333 sequences.

Output File Names:
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.summary

mothur > unique.seqs(fasta=current)
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.fasta as input file for the fasta parameter.
333 333

Output File Names:
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.names
R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.fasta

mothur > get.current()

Current RAM usage: 2.39285 Gigabytes. Total Ram: 15.4159 Gigabytes.

Current files saved by mothur:
fasta=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.fasta
group=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.groups
name=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.names
oligos=CXMicroMothurOligos.txt
qfile=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.qual
processors=8
summary=R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.summary

Current default directory saved by mothur: /usr/bin/

Current working directory: /home/cxlab/Downloads/JalynsLinuxMothurAttemptsFiles/JalynsMothurAttemptsLinux1/

Output File Names:
current_files.summary

mothur > summary.seqs(fasta=current, name=current, group=current, processors=8)
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.fasta as input file for the fasta parameter.
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.groups as input file for the group parameter.
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.names as input file for the name parameter.
group is not a valid parameter.
The valid parameters are: fasta, summary, contigsreport, alignreport, name, count, processors, seed, inputdir, and outputdir.

Using 8 processors.
[ERROR]: did not complete summary.seqs.

mothur > summary.seqs(fasta=current, name=current, groups=current, processors=8)
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.unique.fasta as input file for the fasta parameter.
[ERROR]: mothur does not save a current file for groups
Using current as input file for the groups parameter.
Using R_2021_10_05_12_00_01_user_S5-70-10-05-2021_Chip.trim.names as input file for the name parameter.
groups is not a valid parameter.
The valid parameters are: fasta, summary, contigsreport, alignreport, name, count, processors, seed, inputdir, and outputdir.

Using 8 processors.
[ERROR]: did not complete summary.seqs.
quitting mothur

Hello!

It is said in the command. Just remove group. I believe you wanted the count table ,which is the count parameter to use and not the group parameter.

Have a nice day.

Thank you! This worked!

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