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.