Header Leaderboard Ad

Collapse

stampy hash table overfull

Collapse

Announcement

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

  • stampy hash table overfull

    Hey, I'm new to bioinformatics and currently trying to build a hash table for a reference genome using stampy.

    I have built the .stdix file already and the command that's giving me trouble is:

    python /data/gavin/apps/stampy-1.0.22/stampy.py -g mdo_ref -H mdo_ref 2>mdo_ERR

    I've gone through this pipeline with a few other genomes that haven't caused problems, but I keep getting this error with this genome:

    stampy: Error: hash reached fill factor 0.980000019073 - aborting
    stampy: Now at locus 2413581345 of 3502392093 with stride 5; hash table size is 29 bits
    stampy: Suggest increasing stride or hash table size

    stampy: Error: Overfull hash table


    Would someone be able to tell me how to increase either of these things? The process is getting about 88% complete before stopping and outputting this error.

    Thank you!

Latest Articles

Collapse

  • seqadmin
    How RNA-Seq is Transforming Cancer Studies
    by seqadmin



    Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...
    09-07-2023, 11:15 PM
  • seqadmin
    Methods for Investigating the Transcriptome
    by seqadmin




    Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.

    Whole Transcriptome RNA-seq
    Whole transcriptome sequencing...
    08-31-2023, 11:07 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 09:05 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-21-2023, 06:18 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-20-2023, 09:17 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-19-2023, 09:23 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Working...
X