Question: velvetg failed during the assembly
0
gravatar for slimane.khayi
2.0 years ago by
France
slimane.khayi40 wrote:

Dear all, I have problem during my denovo assembly process,

I have launched velveth for mypaired.fastq containing 600 millions reads in total (length 150) :

velveth out_21 21 -fastq -shortpaired mypaired.fastq

for this steps all were ok

then I launched velvetg on out_21/:

velvetg out_21 -scaffolding no -min_contig_lgth 2000

unfortunately I had this error :

[0.000000] Reading roadmap file out_21/Roadmaps velvetg: Can't calloc 18446744071893837925 Annotations totalling 18446744044658132560 bytes: Cannot allocate memory

have you any ideas about this error? how can i fix it ? thank you in advance .

denovo velvet n50 illumina • 758 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by slimane.khayi40
2
gravatar for toralmanvar
2.0 years ago by
toralmanvar830
toralmanvar830 wrote:

Couple of months back, I also encountered the same error and I didnt get any solution. Similar issue is posted on velvet github issue page but there is no answer to it.

However, when I used older version of velvet (precisely 1.1.07), it solved my problem. So you can also use your velveth result as input for older velvetg version.

ADD COMMENTlink written 2.0 years ago by toralmanvar830

great answer. This has saved my run too. thanks a lot

ADD REPLYlink written 7 months ago by Assa Yeroslaviz1.2k
0
gravatar for slimane.khayi
2.0 years ago by
France
slimane.khayi40 wrote:

thank you for your answer, I'll try it.

ADD COMMENTlink written 2.0 years ago by slimane.khayi40

Did it work? I have the same trouble with 1.2.10

ADD REPLYlink written 4 months ago by tobytaogf0
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