mothur

[ERROR]: name mismatch in pcr.seqs.


#1

Hi there,

I was running pcr.seqs on Silva.nr_v128, for 16S-V4 when I got the error, but only if I use oligos and keepdots=F at the same time

None of these give errors:

mothur "#pcr.seqs(fasta=silva.nr_v128.align, taxonomy=silva.nr_v128.tax, oligos=oligos.txt, processors=4)"

mothur "#pcr.seqs(fasta=silva.nr_v128.align, taxonomy=silva.nr_v128.tax, start=13862, end=23444, keepdots=F, processors=4)"

mothur "#pcr.seqs(fasta=silva.nr_v128.align, taxonomy=silva.nr_v128.tax, start=13862, end=23444, processors=4)"

But this gives one error, per each sequence that would be kept

mothur "#pcr.seqs(fasta=silva.nr_v128.align, taxonomy=silva.nr_v128.tax, oligos=oligos.txt, processors=4, keepdots=F)"

Any idea what happens?

Xabi

PS: the command runs fine until the very end and the errors appear right before the message of

Removed 40387 sequences from your taxonomy file.

Which btw is the correct number of seqs expected to be removed


#2

I forgot to mention that I’m using mothur 1.39.5 in Ubuntu 16.04

Just in case, the problem occurs either if I run from bash via mothur “#pcr.seqs()” or from within mothur


#3

Can you copy an example of the error messages?


#4

Hi Pat,

Here you have. I just trimmed the ~150000 identical error messages, otherwise it is the complete logfile.

Xabi

Linux version

Using ReadLine

Running 64Bit Version

mothur v.1.39.5
Last updated: 3/20/2017

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://www.mothur.org/forum

Type 'quit()' to exit program
Script Mode


mothur > pcr.seqs(fasta=../../ramac/silva.nr_v128.align, taxonomy=../../ramac/silva.nr_v128.tax, oligos=oligos.txt, processors=4, keepdots=F)

Using 4 processors.
[ERROR]: name mismatch in pcr.seqs.
[...]
[ERROR]: name mismatch in pcr.seqs.
Removed 40387 sequences from your taxonomy file.

Output File Names: 
../../ramac/silva.nr_v128.pcr.align
../../ramac/silva.nr_v128.bad.accnos
../../ramac/silva.nr_v128.scrap.pcr.align
../../ramac/silva.nr_v128.pcr.tax


It took 106 secs to screen 190661 sequences.

mothur > quit()


************************************************************
************************************************************
************************************************************
Detected 150273 [ERROR] messages, please review.
************************************************************
************************************************************
************************************************************

#5

Could you post the oligos file?


#6

Now that you mention, I changed the format of the oligos file for testing and now it doesn’t produce an error
I was using the single-line style

primer GTGCCAGCMGCCGCGGTAA GGACTACHVGGGTWTCTAAT V4

So I changed it to the long format and now runs without error messages

forward GTGCCAGCMGCCGCGGTAA
reverse GGACTACHVGGGTWTCTAAT

#7

Great, thanks for posting your solution!