make contigs error

Feature requests
1

Hi Dr.Schloss,
I’m following your MiseqSOP to analyze my microbiome data. While I was struggling with the very first command “make. contigs” recently and I don’t know what’s going on with my codes. I formatted everything exactly follow your tutorial examples. I changed all gz files to fsatq and made the stability. files as illustrated. But there is always a running error which is posted as below. My sequences are already demultiplexed so there should be no problem with barcodes or primer sequences. I am really sorry for asking so basic questions since I am new to these stuff and will appreciate any kind of help. thanks very much in advance. I can share my data with you in dropbox if needed. thanks again!!!




mothur v.1.36.1 Last updated: 7/27/2015

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, co
mmunity-supported software for describing and comparing microbial communities. A
ppl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

Type ‘quit()’ to exit program



mothur > make.contigs(file=stability.files,processors=8)
Using 8 processors.

Processing file pair Day0-154_S41_L001_R1_001.fastq - Day0-154_S41_L001_
R2_001.fastq (files 1 of 54) <<<<<
Making contigs…
[WARNING]: reading ▼ :diamonds: expected a name with @ as a leading character, ignori
ng read.
[WARNING]: reading o╡╬╦ó┘╓═j:^▀ expected a name with + as a leading character, i
gnoring.[WARNING]: names do not match. read ▼ :diamonds: for fasta and o╡╬╦ó┘╓═j:^▀ f
or quality, ignoring.[WARNING]: Lengths do not match for sequence ▼ :diamonds:. Read
48 characters for fasta and 2 characters for quality scores, ignoring read.[ERRO
R]: finding negative quality scores, do you have the right format selected? http
://en.wikipedia.org/wiki/FASTQ_format#Encoding
[WARNING]: reading ▼ :diamonds: expected a name with @ as a leading character, ignori
ng read.
[WARNING]: reading ,^+ expected a name with + as a leading character, ignoring.[
WARNING]: names do not match. read ▼ :diamonds: for fasta and ,^+ for quality, ignori
ng.[WARNING]: Lengths do not match for sequence ▼ :diamonds:. Read 18 characters for
fasta and 5 characters for quality scores, ignoring read.[ERROR]: finding negati
ve quality scores, do you have the right format selected? http://en.wikipedia.or
g/wiki/FASTQ_format#Encoding
1

It took 0 secs to assemble 0 reads.

It took 4 secs to process 0 sequences.

2

I work for Pat Schloss on the mothur project and would be happy to help. From your log file output above, it looks like the files did not decompress properly. Could they still be in *.gz format? When you decompressed them did you run something like:

This command will find and decompress all files ending in .gz
yourFolder yourUserName$ find . -name “*.gz” -exec gunzip {} ;

Conversely, this command will find and compress all fastq files.
yourFolder yourUserName$ find . -name “*.fastq” -exec gzip {} ;

3

Hi @westcott,

I have the same error. I have installed last versions of both mothur and zlib (both i686 & x86_64) on my CentOS. However, I’m still getting the same error.

4

Could you send your log file and a pair of the fastq files to mothur.bugs@gmail.com?