Hi I am running meta-velvetg for de novo assembly on a metagenome with 47 million reads from an Illumina HiSeq paired-end run (101bp sequence reads). I successfully ran velveth with a k-mer length of 31 and velvetg insert length of 184 (the average after combining the forward and reverse pairs).
When I get to meta-velvetg, I run the code:
meta-velvetg 7811_velveth -ins_length 184 | tee 7811_velveth/log
After running the code I get the following output:
[meta-velvetg] Check command line options... OK. Your command line options seem to be good. [meta-velvetg] Load meta-graph ... [0.000000] Reading read set file 7811_velveth/Sequences; [6.666332] 47737003 sequences found [6.671167] Read 17 of length 32788, longer than limit 32767 [6.671172] You should modify recompile with the LONGSEQUENCES option (cf. manual)
I tried the “make ‘LONGSEQUENCES=1’” option, but I get the same error. Also, looking at the contigs.fa file, read 17 is 187 bp, not 32788. I searched for a contig of length 32788 but couldn’t find one. The longest I found was 4788. Any help would be greatly appreciated!