Question: meta-velvetg exceeding read length limit
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gravatar for millera25
3.0 years ago by
millera250
millera250 wrote:

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!

assembly • 893 views
ADD COMMENTlink modified 3.0 years ago by genomax74k • written 3.0 years ago by millera250

Did you do a make clean before recompiling? Just checking.

ADD REPLYlink written 3.0 years ago by genomax74k
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