jellyfish histo is empty
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Entering edit mode
3 months ago
m.t.lorenc • 0

I ran Jellyfish

> zcat V*_R1.fastp.fq.gz | jellyfish count -t 2 -C -m 21 -s 5G --quality-start=33 -o reads.jf
> cat reads.jf 
000001535{"alignment":8,"canonical":true,"cmdline":["count","-t","2","-C","-m","21","-s","5G","--quality-start=33","-o","reads.jf"],"counter_len":4,"exe_path":"/mnt/hpccs01/work/x/miniconda2/envs/jellyfish/bin/jellyfish","format":"binary/sorted","hostname":"cl5n014","key_len":42,"matrix1":{"c":42,"columns":[7114389000,2192333556,7375600293,3957177567,1753639420,5791419737,7660672264,3955008356,2531272710,4865888693,6095688361,6974692332,2128614574,2258809230,885814170,1703365744,5945426963,375951490,7217126865,6145592432,7418978358,2071372677,3810558711,7150470371,5456096994,5475478,7949231332,5100019741,6318414384,7141154869,3543742516,6024410566,5605745954,575704984,8124532068,1053004640,2675922405,1674046033,5535382637,1853889752,1425936082,3907867046],"identity":false,"r":33},"max_reprobe":126,"pwd":"/mnt/hpccs01/scratch/x/y/fastpDNA","reprobes":[1,1,3,6,10,15,21,28,36,45,55,66,78,91,105,120,136,153,171,190,210,231,253,276,300,325,351,378,406,435,465,496,528,561,595,630,666,703,741,780,820,861,903,946,990,1035,1081,1128,1176,1225,1275,1326,1378,1431,1485,1540,1596,1653,1711,1770,1830,1891,1953,2016,2080,2145,2211,2278,2346,2415,2485,2556,2628,2701,2775,2850,2926,3003,3081,3160,3240,3321,3403,3486,3570,3655,3741,3828,3916,4005,4095,4186,4278,4371,4465,4560,4656,4753,4851,4950,5050,5151,5253,5356,5460,5565,5671,5778,5886,5995,6105,6216,6328,6441,6555,6670,6786,6903,7021,7140,7260,7381,7503,7626,7750,7875,8001],"size":8589934592,"time":"Wed Nov 22 14:46:48 2023","val_len":7}

However, when I ran jellyfish histo -t 2 reads.jf > reads.histo. The output is empty. What did I miss?

jellyfish kmer fastq • 185 views
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