search

natapol / kitsune

a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.
GNU General Public License v3.0
10 stars 3 forks source link

truncated bloom filter #15

Open SkiZeus opened 2 months ago

SkiZeus commented 2 months ago

when attempting kitsune cre on fasta file:

(rgiDev) wlodarsm@ascension:/workspace/lab/mcarthurlab/wlodarsm/kitsune/test$ kitsune cre --filename test.fasta -o cre_out -ke 20 0%| | 0/17 [00:02<?, ?it/s] Traceback (most recent call last): File "/home/wlodarsm/mambaforge-pypy3/envs/rgiDev/lib/python3.10/site-packages/kitsune/modules/kitsunejf.py", line 244, in init datadict[dat[0]] = int(dat[1]) ValueError: invalid literal for int() with base 10: 'filter'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/wlodarsm/mambaforge-pypy3/envs/rgiDev/bin/kitsune", line 8, in sys.exit(main()) File "/home/wlodarsm/mambaforge-pypy3/envs/rgiDev/lib/python3.10/site-packages/kitsune/kitsune.py", line 71, in main module.run(sys.argv) File "/home/wlodarsm/mambaforge-pypy3/envs/rgiDev/lib/python3.10/site-packages/kitsune/modules/cre.py", line 116, in run outdata = cal_cre(args.filename, vars(args)) File "/home/wlodarsm/mambaforge-pypy3/envs/rgiDev/lib/python3.10/site-packages/kitsune/modules/cre.py", line 55, in cal_cre a0 = jf.Kmercount(fsa, kmer, karg) File "/home/wlodarsm/mambaforge-pypy3/envs/rgiDev/lib/python3.10/site-packages/kitsune/modules/kitsunejf.py", line 247, in init raise JellyFishError("Bloom filter file is truncated.") kitsune.modules.kitsunejf.JellyFishError: Bloom filter file is truncated.