velvetg failed during the assembly

Question

[slimane.khayi]

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 .

Answer 1

[Tm]

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.

[Assa Yeroslaviz]

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

Answer 2

[slimane.khayi]

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

[tobytaogf]

Did it work? I have the same trouble with 1.2.10