Question: Running velveth with multiple k-mer lengths: process stops after first k-mer value
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Ty • 0 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!
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
writeaccess permissions for this directory?