I’m trying to use the make.contigs command together with gzipped fastq files to save on disk space.
For some pairs of fastq.gz files, which come straight from a MiSeq, I’m getting millions of warnings like
[WARNING]: missing sequence for , ignoring.[WARNING]: expected a name with + as a leading character, ignoring.[WARNING]: missing quality for , ignoring.[WARNING]: Blank fasta name, ignoring read.
from mothur which then slowly tries to use up all avaiable memory. Other gzipped files from the same MiSeq run process normal, without warnings. When I first gunzip those problematic files all is fine and when recompress them with gzip, on Linux, all goes well too. I used mothur version 1.37.4 on Linux for this.
Let me know if I you need more information.
–Robert
The badly behaving fastq.gz files are all very small, with 61 or fewer reads per sample, but all files (which I’ve tried, from the same MiSeq run) with 202 or more reads work fine.
I’ve copied the relevant part of the log file below. The second line with warnings, having four [WARNING] pieces then gets repeated perpetually.
mothur > make.contigs(file=fileList.paired.file)
Using 1 processors.
Processing file pair /tmp/mothur_test/with_file_original/31M11_S5_L001_R1_001.fastq.gz - /tmp/mothur_test/with_file_original/31M11_S5_L001_R2_001.fastq.gz (files
1 of 1) <<<<<
Making contigs…
[WARNING]: Blank fasta name, ignoring read.
[WARNING]: missing sequence for , ignoring.[WARNING]: expected a name with + as a leading character, ignoring.[WARNING]: missing quality for , ignoring.[WARNING]: Blank fasta name, ignoring read.
Thanks for sending your files. I can reproduce the error, but when I decompress and recompress it the error is gone. Can you see if this works on your end?
mothur > make.contigs(inputdir=…/…/make.contigs, file=file.txt)
Setting input directory to: /Users/sarahwestcott/Desktop/make.contigs/
Using 1 processors.
Processing file pair /Users/sarahwestcott/Desktop/make.contigs/31M11_S5_L001_R1_001.fastq.gz - /Users/sarahwestcott/Desktop/make.contigs/31M11_S5_L001_R2_001.fastq.gz (files 1 of 1) <<<<<
Making contigs…
[WARNING]: Blank fasta name, ignoring read.
[WARNING]: missing sequence for , ignoring.[WARNING]: expected a name with + as a leading character, ignoring.[WARNING]: missing quality for , ignoring.[WARNING]: Blank fasta name, ignoring read.
[WARNING]: missing sequence for , ignoring.[WARNING]: expected a name with + as a leading character, ignoring.[WARNING]: missing quality for , ignoring.[WARNING]: Blank fasta name, ignoring read.
…