Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X