Hi
I am getting an error in unique.seqs command like:
[ERROR]: You already have a sequence named NB501984_42_H7FN2AFX2_2_21112_20285_13267 in your fasta file, sequence names must be unique, please correct.
[ERROR]: NB501984_42_H7FN2AFX2_2_21112_20285_13267 is not in your count table. Please correct.
12347240 801866
However after searching through my fasta file, I did not find any duplicated sequence names… and I am also not sure why the sequence that mentioned in the error was not included in my count file…?
Then I went back and tried to run summary.seqs (fasta=/Volumes/mypassport/mothur-2/EISPmothur2.trim.contigs.fasta)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 30 30 0 2 1
2.5%-tile: 1 99 99 0 3 1019301
25%-tile: 1 141 141 0 4 10193008
Median: 1 168 168 0 4 20386015
75%-tile: 1 168 168 0 4 30579022
97.5%-tile: 1 174 174 2 6 39752729
Maximum: 1 270 270 58 135 40772029
Mean: 1 157 157 0 4
of Seqs: 40772029
It took 1202 secs to summarize 40772029 sequences.
it seems that the sequence number does not match here?
I am using the version1.48 and 8 processors, the upstream command is only make.contigs.
Does anyone kindly know what should I do to fix this problem?
Hello
I want to add some actions I tried here…
I re-ran the make.contigs from the beggining using a 1.44 version of Mothur
and then
unique.seqs (fasta=/Volumes/mypassport/mothur-3/EISPmothur3.trim.contigs.good.fasta) (I re-ran in another directionary for the 1.44mothur)
and more errors went out as **** Exceeded maximum allowed command errors, quitting ****
[ERROR]: You already have a sequence named NB501984_42_H7FN2AFX2_1_21205_25114_6689 in your fasta file, sequence names must be unique, please correct.
so I tried the list.seqs(fasta=/Volumes/mypassport/mothur-3/EISPmothur3.trim.contigs.good.fasta)
and it ended up with tons of warnings as
[WARNING]: We found more than 25% of the bases in sequence !!!H__PAGEZEROx__TEXT?_?___text__TEXT?_Z??__stubs__TEXT to be ambiguous. Mothur is not setup to process protein sequences.
[WARNING]: We found more than 25% of the bases in sequence M?H?[A^A_]?\H?[A^A_]?f?UH??H??H??H??t to be ambiguous. Mothur is not setup to process protein sequences.
[WARNING]: We found more than 25% of the bases in sequence ?H??H??H?U?H?M?E?|$ to be ambiguous. Mothur is not setup to process protein sequences.
and my good.accnos file is zerobyte.
so, could anyone knows what was happening here…?
hi everyone
sorry to bother again!
I closely checked my stability file from the very beginning this time and found I import one of my samples twice…
I think that is where the error came from.
Thank you!!