kmer genie output

Question

[venkataraman.arvind]

Hi,

I am running kmergenie as follows:

/kmergenie reads_list.txt

The file reads_list.txt reads like this:

7A_R1.sickle.fq
7A_R2.sickle.fq

They are all in the same directory. But, kmergenie does not complete. The output stops at:

running histogram estimation
File reads_list.txt starts with character "7", hence is interpreted as a list of file names
Reading 2 read files
Linear estimation: ~4594 M distinct 71-mers are in the reads
K-mer sampling: 1/876
| processing                                                                                         |
[going to estimate histograms for values of k: 121 111 101 91 81 71 61 51 41 31 21 
-------

[WouterDeCoster]

Is the process using memory? Dead? You can have a look at the running processes using tools like top or more pretty htop

[venkataraman.arvind]

Hi Wouter,

Your suspicion is right. The process does not appear to be using any memory.

Arvind

[WouterDeCoster]

I had a brief look at the code and have the impression that the stalling is happening in the specialk step, could you check whether you do have that script (binary) in the kmergenie folder? Does it run (without arguments)?

[venkataraman.arvind]

Thanks Wouter. I checked. The specialk script is present in the kmergenie folder and it runs. Below is the output:

usage: ./specialk reads_file [-o out_prefix] [-s step] details: [-o out_prefix] saves results in [out_prefix].histo [-s step] interval between consecutive kmer sizes (default: 10) [-k value] largest k-mer size to evaluate (default: 121) [-l value] smallest k-mer size to evaluate (default: 15) [-e value] k-mer sampling (default: auto-detected power of 10) [-t value] number of threads (default: 1) Input file can be fasta, fastq, gzipped or not, or a file containing a list of file names. Running ./specialk version 1.7016

[WouterDeCoster]

Well that's as far as I can troubleshoot your issue, probably the developers can help you better...