velvetg not working: no stats.txt output

[rominahenriques]

Hello,

I'm trying to run VelvetOptimizer on four samples with 3 million reads on average (x2 as they are paired-reads). Although velveth works and produces the expected outputs, velvetg seems to be crashing.

This is the input script:
VelvetOptimiser.pl -s 33 -e 121 -t 8 -f '-shortPaired -separate -fastq CNN_R1_val_1.fq CNN_R2_val_2.fq'
and it generates auto_data files from 33 to 12. However, when vanilla velvetg is supposed to run, it crashes.

Example of the error file:
Oct 6 17:11:08 Running vanilla velvetg on hash value: 49
velvetg: Can't calloc 281474976710656 void*s totalling 2251799813685248 bytes: Cannot allocate memory
This happens for the majority of hash values, and the end of the error file says:
Oct 6 17:12:26 Hash value of best assembly by assembly score: 97
Oct 6 17:12:26 Optimisation routine chosen for best assembly: shortPaired
Oct 6 17:12:26 Looking for the expected coverage
Unable to open /home/rhenriques/capensis/Rainbow_Tr50/trimmed/50e001/auto_data_97/stats.txt for exp_cov determination.
at /apps/velvet/1.2.10-9adf09f-KMER121/contrib/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 859.

When I try to run velvetg manually using the script
velvetg /home/rhenriques/capensis/Rainbow_Tr50/trimmed/50e001/auto_data_97

I get this error message:
velvetg: Can't calloc 281474976710656 void*s totalling 2251799813685248 bytes: Cannot allocate memory

Can you please let me know how to proceed?
Thank you!

Cheers,
Romina

[Slugger70]

It looks as though the computer you are running on doesn't have enough memory to complete the assembly unfortunately. Try reducing the number of threads used to 1 to reduce the number of concurrent velvetgs being run and see what happens.