Tweet
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!
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!