Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • 2seq
    Junior Member
    • Oct 2012
    • 9

    #1

    KmerFreq - std::bad_alloc

    I am new to SOAPdenovo and am still learning, so please help out this newbie.
    I am running a PBS script to run KmerFreq before running SOAP. I have two fq files: s_4_1.txt and s_4_2.txt which I list in the list file. I made sure to add a carriage return after the last file in the list. Both files are around 65G. I am running KmerFreq on 1 node and 1 processor and have allocated 100gb of memory. I'm also running this over valgrind so I can determine the needs of the program for some other samples. So the script looks like:

    #PBS -N KmerFreq-PL71 -l nodes=1pn=1,mem=100gb -j oe -m be -M [email protected]
    #PBS -l walltime=12:00:00
    module load valgrind
    module load soapdenovo-1.05
    cp * PFSDIR
    cd $PFSDIR
    valgrind --tool=massif KmerFreq -i PL_list -o PL71_correct
    cp * $PBS_O_WORKDIR

    In checking the log file, I see:
    ==7580==
    quality cutoff: 5
    seed length: 17
    output kmer index?: no
    file format: fq
    terminate called after throwing an instance of 'std::bad_alloc'
    what (): St9bad_alloc
    ==7580==
    -bash: line 7: 7580 aborted

    Any assistance would be greatly appreciated!

Latest Articles

Collapse

  • kinpict.com
    Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by kinpict.com
    The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
    Today, 06:37 PM
  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2





    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
    10-30-2026, 06:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 11-12-2026, 07:59 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-05-2026, 09:25 AM
0 responses
35 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-03-2026, 11:54 AM
2 responses
56 views
0 reactions
Last Post kinpict.com  
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
175 views
0 reactions
Last Post SEQadmin2  
Working...