Greetings!
I have used velvet with success before, but I seem to be missing something this time.
The data is paired-end HiSeq Illumina reads, 100bp (400bp inserts). Velvet is compiled with MAXKMERLENGTH=200, CATEGORIES=10, OPENMP=1.
The command I am using:
The hash directories are formed for each kmer length, but they just come out with the following files: Log, Sequence, Roadmap -- no contigs, no stats, nothing else.
The sequences appear to be loading, the end of the standard output is:
Any idea what I am doing wrong?
Thanks!
I have used velvet with success before, but I seem to be missing something this time.
The data is paired-end HiSeq Illumina reads, 100bp (400bp inserts). Velvet is compiled with MAXKMERLENGTH=200, CATEGORIES=10, OPENMP=1.
The command I am using:
Code:
velvet_1.2.10/velveth Assembly1 53,91,8 -shortPaired -separate -fastq HiSeq_100_R1.trimmed.fastq.pe HiSeq_100_R2.trimmed.fastq.pe
The sequences appear to be loading, the end of the standard output is:
Code:
...... [1262.752392] Inputting sequence 84000000 / 112022250 [1265.931838] Inputting sequence 42000000 / 112022250 [1266.165014] Inputting sequence 28000000 / 112022250 [1266.716441] Inputting sequence 14000000 / 112022250 [1299.839334] === Sequences loaded in 399.530517 s [1299.845389] Done inputting sequences [1299.845391] Destroying splay table [1302.434467] Splay table destroyed done
Thanks!
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