Question: Running velveth with multiple k-mer lengths: process stops after first k-mer value
gravatar for Ty
2.4 years ago by
United States
Ty0 wrote:

I am running velveth for de novo assembly of a paired-end sequence set of ~59.8 million sequences (Illumina HiSeq4000, 150bp) at a range of k-mer lengths (21 to 41), using the following command:

./velveth /path-to-output/ 21,41,2 -fastq -shortPaired -separate /path-to-sequence-files/forwardseqs.fastq /path-to-sequence-files/reverseseqs.fastq

velvet (1.2.10) was compiled with 'MAXKMERLENGTH=61'. Velvet and the sequence files are in different directories.

Everything works fine for the first k-mer value. velvet then creates a folder for the next k-mer value and creates a Log file, but then quits. The screen output, beginning with the last part of the sequence input, is as follows:

 [2554.339432] Inputting sequence 5900000 / 59845752 

 [2585.427939] === Sequences loaded in 2133.454707 s 

 [2585.527645] Done inputting sequences 

 [2585.527671] Destroying splay table 

 [2586.257082] Splay table destroyed 

 rm: data: is a directory 

 [2586.612381] Command failed!

 [2586.612389] rm -f /path-to-sequence-files/_23/Sequences

The shell then returns to the shell prompt with no further output.

Help appreciated!

velvet assembly • 1.0k views
ADD COMMENTlink written 2.4 years ago by Ty0

Can you list the contents of the directory from which you are running velveth? The line rm: data: is a directory in the output looks suspicious. Do you have write access permissions for this directory?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Kevin Blighe65k
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