I am encountering a problem during trim.seqs (version 1.31.2…64-bit, MPI enabled). I am splitting ion torrent reads labeled with dual barcodes (one at the start of the read and one at the end of the read) using this command:
trim.seqs(fasta=nofilter.fasta, qfile=nofilter.qual, oligos=steph_oligos, checkorient=T, maxhomop=8, maxambig=2, qaverage=20, qwindowaverage=20, processors=10, minlength=200, bdiffs=1, pdiffs=2)
I am occasionally see these when the program is running:
[ERROR]: std::bad_alloc has occurred in the QualityScores class function trimQScores. This error indicates your computer is running out of memory. This is most commonly caused by trying to process a dataset too large, using multiple processors, or a file format issue. If you are running our 32bit version, your memory usage is limited to 4G. If you have more than 4G of RAM and are running a 64bit OS, using our 64bit version may resolve your issue. If you are using multiple processors, try running the command with processors=1, the more processors you use the more memory is required. Also, you may be able to reduce the size of your dataset by using the commands outlined in the Schloss SOP, http://www.mothur.org/wiki/Schloss_SOP. If you are uable to resolve the issue, please contact Pat Schloss at firstname.lastname@example.org, and be sure to include the mothur.logFile with your inquiry.
And also these errors when the program is compiling output.
Appending files from process 5839
Appending files from process 5840
Appending files from process 5841
[ERROR]: Could not open /data2/sgeiboverflow/FungusMetagenomics/nofilter.fasta5841.num.temp
Appending files from process 5842
Appending files from process 5843
Appending files from process 5844
[ERROR]: Could not open /data2/sgeiboverflow/FungusMetagenomics/nofilter.fasta5844.num.temp
Appending files from process 5845
Appending files from process 5846
Appending files from process 5847
[ERROR]: Could not open /data2/sgeiboverflow/FungusMetagenomics/nofilter.fasta5847.num.temp
If I proceed anyhow, I get errors about sequences being in my group file, but not my fasta file. This machine has 250 Gb RAM, the fasta/qual files have only 7 million sequences in it, and there are no other processes running. I don’t think the machine could really be running out of memory? Changing the number of processors (more/less) does not fix this error.
Any ideas about what could be causing this? Thanks so much for your help!