Jellyfish histo produces a blank file
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Entering edit mode
21 months ago
mln.mrt • 0

I am trying to estimate genome size of a species with high coverage Illumina data with jellyfish using the following arguments:

jellyfish count -t 16 -C -m 17 -s 5G -o 17mer-out --min-quality=20 file1.fastq file2.fastq

But when i try to produce the histogram of kmer count with:

jellyfish histo -o 17mer-out.histo 17mer-out

I obtain a blank file "17mer-out.histo

What i am doing wrong?

jellyfish version: 2.3.0

17mer-out file contains

000001455{"alignment":8,"canonical":true,"cmdline":["count","-t","16","-C","-m","17","-s","5G","-o","17mer-out","--min-quality=20","seq1.fq","seq2.fq"],"counter_len":4,"exe_path":"/usr/bin/jellyfish","format":"binary/sorted","hostname":"bioinformatica","key_len":34,"matrix1":{"c":34,"columns":[7196745473,7301074138,2132658977,5020955328,3333575821,7282503335,871864227,2747768770,5239399186,3828180330,2513005616,2747700235,7223253862,378647116,1521242413,3093383940,8372980947,5997395473,244185457,5353416976,455426711,233275036,4469277497,4352995626,3111999401,2627462674,2662475798,997259155,5476537116,3709366776,767206678,691159434,6385758751,8192433938],"identity":false,"r":33},"max_reprobe":126,"path":[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":"Tue
Feb 25 15:44:32 2020","val_len":7}
size jellyfish genome • 570 views
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Is the above output all there is in the 17mer-out file? What is the output of tail -n1 17mer-out, and what is the size of the 17mer-out file? If this file doesn't contain anything beyond this header, the count step didn't finish successfully.

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Hi, I have the same problem and I have a normal mer_output file. Did you find out how to fix it?

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