Tried running unique.seqs with fasta and names file made from the fasta using list.seqs. It gave me this error. However the sequences are in the name file. I checked and double checked.
mothur > unique.seqs(fasta=/Volumes/GRAID/GoM_biog/Cooked5th6/GGALIGN/GG.trim.align, name=/Volumes/GRAID/GoM_biog/Cooked5th6/GGALIGN/Greenegenes.trim.names) [ERROR]: 19-AB5-B12-28F__H3UPEKF02EM8OZ is in your fasta file, and not in your namefile, please correct. [ERROR]: 19-AB5-B12-28F__H3UPEKF02D7D49 is in your fasta file, and not in your namefile, please correct. [ERROR]: 19-AB5-B12-28F__H3UPEKF02D1DYW is in your fasta file, and not in your namefile, please correct. [ERROR]: 19-AB5-B12-28F__H3UPEKF02D245Q is in your fasta file, and not in your namefile, please correct. [ERROR]: 19-AB5-B12-28F__H3UPEKF02EJSLJ is in your fasta file, and not in your namefile, please correct. . . . This continues with pretty much all my sequences.
The sequences are all there I checked, They are not duplicated. I ensured it is all in Plain txt without any special characters.
I made the name file using list.seqs from the fasta file then tried running unique seqs. It gave me same error… So i tried running a different command(summary.seqs)
after giving up using the names file in summary.seqs i ran it just by fasta this is what it told me:
mothur > summary.seqs(fasta=/Volumes/GRAID/GoM_biog/Cooked5th6/GGALIGN/GG.trim.align)
Using 1 processors.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is /Volumes/GRAID/GoM_biog/Cooked5th6/GGALIGN/GG.trim.accnos which seems to match /Volumes/GRAID/GoM_biog/Cooked5th6/GGALIGN/GG.trim.align.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 95 111 4 0 2 1
2.5%-tile: 138 1855 293 0 4 3002
25%-tile: 138 2054 407 0 5 30018
Median: 138 2217 449 0 5 60035
75%-tile: 138 2260 477 0 5 90052
97.5%-tile: 138 2264 510 1 6 117068
Maximum: 6846 6852 622 1 8 120069
Mean: 138.521 2157.27 435.853 0.0473644 4.90116
of Seqs: 120069
Output File Names:
/Volumes/GRAID/GoM_biog/Cooked5th6/GGALIGN/GG.trim.summary
.
.
.
So it can use the file just not when I command it too.
I tried to use the file in chimera.uchime command and it too failed. saying
missing name 21-AB5-N12-28F__H3DHL2N04JXCXS
missing name 21-AB5-N12-28F__H3DHL2N04JXJTT
missing name 21-AB5-N12-28F__H3DHL2N04JXM45
missing name 21-AB5-N12-28F__H3DHL2N04JXSM7
missing name 21-AB5-N12-28F__H3DHL2N04JXYTH
missing name 21-AB5-N12-28F__H3DHL2N04JY3IO
missing name 21-AB5-N12-28F__H3DHL2N04JYCHJ
missing name 21-AB5-N12-28F__H3DHL2N04JYFY9
missing name 21-AB5-N12-28F__H3DHL2N04JYKKT
missing name 21-AB5-N12-28F__H3DHL2N04JYNP0
missing name 21-AB5-N12-28F__H3DHL2N04JYSAB
missing name 21-AB5-N12-28F__H3DHL2N04JYYNL
missing name 21-AB5-N12-28F__H3DHL2N04JZGMM
missing name 21-AB5-N12-28F__H3DHL2N04JZMM3
missing name 21-AB5-N12-28F__H3DHL2N04JZS9H
missing name 21-AB5-N12-28F__H3DHL2N04JZTGA
missing name 21-AB5-N12-28F__H3DHL2N04JZYU5
.
.
.
so on and so forth
So I ran the protocol without a names file and it created one by auto-running unique.seqs it made the following outputs of a fasta and names file. I presume it used these two output to auto-proceed with the chimera.chime command.