trim.seqs [ERROR]

mothur bugs
1

So I have a fasta, names, and oligos file. I made the names file from the fasta file using the command unique.seqs. Now when I am trying to perform a trim.seqs command, it continues to give me this error for multiple headers in my names file.

[ERROR]: (header) is not in your namefile, please correct.

I have checked out my names file and it seems to have the many headers it says do not exist in my names file. I am not sure what to do.

2

The names file shouldn’t have a header. Can you paste in the commands exactly as you are running them?

Pat

3 
mothur > trim.seqs(fasta=Cleanedmosquitodev.fasta, name=Cleanedmosquitodev.names, oligos=Cleanedmosquitodev.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=2)
4

Here is a step by step method of how i received my input files:

  1. I obtained a fasta file from an NCBI article
  2. I ran the following code to generate a Name file from the fasta file:
unique.seqs(fasta=Cleanedmosquitodev.fasta)
  1. I created an oligos file by obtaining the forward and reverse primers from the following website along with the appropriate barcodes https://www.ncbi.nlm.nih.gov/sra/SRX447482[accn]
  2. Then I ran the following command:
trim.seqs(fasta=Cleanedmosquitodev.fasta, name=Cleanedmosquitodev.names, oligos=Cleanedmosquitodev.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=2)

and I received the following error:
[ERROR]: SRR1141111271062 is not in your namefile, please correct.
[ERROR]: SRR1141111271102 is not in your namefile, please correct.
[ERROR]: SRR1141111271152 is not in your namefile, please correct.
[ERROR]: SRR1141111271172 is not in your namefile, please correct.
[ERROR]: SRR1141111271182 is not in your namefile, please correct.
[ERROR]: SRR1141111271222 is not in your namefile, please correct.
[ERROR]: SRR1141111271232 is not in your namefile, please correct.
[ERROR]: SRR1141111271262 is not in your namefile, please correct.
[ERROR]: SRR1141111271282 is not in your namefile, please correct.
…this continues for a while

5

You likely want to run this instead…

trim.seqs(fasta=Cleanedmosquitodev.unique.fasta, name=Cleanedmosquitodev.names, oligos=Cleanedmosquitodev.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=2)