[ERROR]: std::bad_alloc has occurred

mothur bugs
1

Hi, Please consider below error. I upgraded laptop with following configuration (intel ® Core i5 -7200U @ 2.50GHz, 8GB RAM with 250GB SSD hard drive) but still not able to align…

############################################################################
mothur >
align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.nr_v128.align)

Using 1 processors.

Reading in the silva.nr_v128.align template sequences… [ERROR]: std::bad_alloc has occurred in the Sequence class function Sequence. 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 mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.

2

The reference file is over 8G and will not fit in RAM. You can reduce the size of the reference by isolating the region. Pat gives an example of this in the MISeq_SOP.

"Now we need to align our sequences to the reference alignment. Again we can make our lives a bit easier by making a database customized to our region of interest using the pcr.seqs command. To run this command you need to have the reference database (silva.bacteria.fasta) and know where in that alignment your sequences start and end. To remove the leading and trailing dots we will set keepdots to false. You could also run this command using your primers of interest.:

mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F, processors=8)"

3

Hi, I think 8G RAM is not issue for 8G reference database. I run Mothur at “align.seqs” command and my laptop used memory showing ~4G out of 8G. Also, the pipeline is taking so much time at the command “chimera.uchime” to removing chimera from a 245MB fastq file. Could you let me know usually how long time takes pipeline to perform command “chimera.uchime” with the same size fastq file.

Here is “System performance”::
###Task Manager####

CPU:
36% 3.09 GHz

Memory:
4.4/7.9 GB (56%)

4

Hi,

The pipeline is taking so much time (~105h) at the command “chimera.uchime” to removing chimera from a total 24 samples fastq file (2GB). Please let me know usually how long time takes pipeline to perform command “chimera.uchime” with the same size fastq file. I upgraded my system with the 8GB RAM, i5 Intel, SSD hard-drive. Thanks

5

How deeply sequenced are each of those samples? Uchime times are dependent on the depth of sequencing in a sample, and the number of rare/singleton sequences you have.