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Old 08-04-2016, 11:05 AM   #1
mes_microbe
Junior Member
 
Location: ashford ct, USA

Join Date: Aug 2016
Posts: 1
Question MetaVelvet crashes, no error given

Hello everyone,

I'm currently experimenting with different assembly programs with a small metagenomic dataset (~4 million reads) and I would like to try out Metavelvet but it seems to crash on me when I use the whole dataset.

I'm using Illumina paired end reads that are 251 bp long from a library prepared using NexteraXT. I have ~2 million forward and 2 million reverse reads so not much considering its a metagenomic data set.

I've tried out metavelvet using both the developer's small sample dataset as well as 500,000 of my own reads and they both assemble just fine. However, when I try to use the entire dataset it crashes at steps after using the meta-velvetg command.

The program is installed on a cluster and I'm using a high memory node to run the program.

Here are the commands I use:

velveth outdir_metav 47 -fasta -shortPaired R1.fasta R2.fasta

velvetg outdir_metav -exp_cov auto -ins_length 251;

meta-velvetg outdir_metav -ins_length 251 | tee logfile;

I understand that the higher the kmer size you use, the more memory the program requires to run so I've also tried re-running the program with different kmer sizes (35, 47, 53, and 61) and all of them seem crash.

I also tried to pair the reads and then split the file up such that every input file had fewer than 1 million reads in it. That also didn't work.

I've looked through forums and emailed the developers and have had no luck finding out what the issue is. I even had the program installed!

If anyone has any advice I would appreciate it!
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assemblers, bioinfomatics, illumina, metagenomic, metavelvet

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