Hello
I am using Ubuntu 64-bit 14.04 LTS with 32 Gb of RAM and running Velvet v1.2.10 and MetaVelvet v1.2.02 with MAXKMERLENGTH=31. I have the following problem: MetaVelvet gets stuck at the "Pebble resolution" (scaffoliding) step when trying to assemble contigs from a test dataset of 100000 Illumina MiSeq 2x300 PE reads, which were not processed in any way (no trimming, adapter removal etc.). After reaching "Starting pebble resolution..." step meta-velvetg gets stuck for indeterminable amount of time with one core showing 100% load. The last time I tried to test it I waited for more than 12 hours before killing the process manually.
I also tried to use MetaVelvet as one of the assemblers in the MetAMOS pipeline and it froze with the same symptoms at the (probably) same step.
$ meta-velvetg Assem -ins_length 350 [meta-velvetg] Check command line options... OK. Your command line options seem to be good. [meta-velvetg] Load meta-graph ... [0.000001] Reading read set file Assem/Sequences; [0.048786] 200000 sequences found [0.222462] Done [0.593372] Reading graph file Assem/Graph2 [0.593503] Graph has 148377 nodes and 200000 sequences [meta-velvetg] Category = 'short1' Ave. = 350, SD = 35 [meta-velvetg] Category = 'short2' Ave. = -1, SD = -1 [meta-velvetg] Category = 'long' Ave. = -1, SD = -1 [meta-velveth] ...done (load meta-graph). [meta-velvetg] Estimate coverage parameters... [mate-velvetg] Estimate expected coverage ... yes. Expected coverage = 1.87805 [mate-velvetg] Estimate expected coverages ... yes. [1.431262] Writing into stats file Assem/meta-velvetg.Graph2-stats.txt... [MetaHisto] First valley = 2 [MetaHisto] Largest peak coverage = 2 (frequency count = 6.35635e+06) [MetaHisto] Noise cutoff coverage = 635635 [meta-velvetg] Warning: Can't find multiple coverage peaks. [meta-velvetg] Trun on single coverage peak mode. [MetaGraph] 1-th coverage peak = 1.87805 [meta-velvetg] Estimate coverage cutoff ... yes. Coverage cutoff = 0.939024 [meta-velvetg] ...done (estimate coverage parameters). [meta-velvetg] Remove low & high coverage nodes ... [meta-velvetg] Min. coverage cutoff for short reads = 0.939024 [meta-velvetg] Min. coverage cutoff for long reads = -1 [meta-velvetg] Max. coverage cutoff for short & long reads = -1 [meta-velvetg] Min. contig length = -1 [VelvetGraph] === Remove low coverage nodes === [1.642372] Removing contigs with coverage < 0.939024... [1.645049] Concatenation... [1.655673] Renumbering nodes [1.655685] Initial node count 148377 [1.656127] Removed 0 null nodes [1.656145] Concatenation over! [1.659085] Concatenation... [1.669341] Renumbering nodes [1.669351] Initial node count 148377 [1.669692] Removed 0 null nodes [1.669698] Concatenation over! [VelvetGraph] === Remove high coverage nodes === [VelvetGraph] === Clip tips hardly === [1.669714] Clipping short tips off graph, drastic [1.675634] Concatenation... [1.686590] Renumbering nodes [1.686609] Initial node count 148377 [1.686959] Removed 0 null nodes [1.686967] Concatenation over! [1.686984] 148377 nodes left [meta-velvetg] ...done (remove low & high coverage nodes). [meta-velvetg] Scaffolding based on paired-end information ... [MetaGraph] === Scaffolding with single peak mode === [VelvetGraph] === Rock Bank === [1.687007] Read coherency... [1.690673] Identifying unique nodes [1.693808] Done, 82558 unique nodes counted [1.693821] Trimming read tips [1.701690] Renumbering nodes [1.701704] Initial node count 148377 [1.702079] Removed 0 null nodes [1.702087] Confronted to 0 multiple hits and 0 null over 0 [1.702092] Read coherency over! [VelvetGraph] === Create read paring array === [VelvetGraph] === Detach dubious reads === [VelvetGraph] === Activate gap markers === [VelvetGraph] === Scaffolding === [1.703117] Starting pebble resolution...
Any help would be really appreciated.