Diamond error :Failed to allocate sufficient memory. Please refer to the manual for instructions on memory usage.

Question

[Ap1438]

Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 32
On-line CPU(s) list: 0-31
Thread(s) per core: 2
Core(s) per socket: 4
Socket(s): 4
NUMA node(s): 4
Vendor ID: GenuineIntel
CPU family: 6
Model: 45
Model name: Intel(R) Xeon(R) CPU E5-4603 0 @ 2.00GHz
Stepping: 7
CPU MHz: 1971.637
CPU max MHz: 2000.0000
CPU min MHz: 1200.0000
BogoMIPS: 3999.58
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 10240K
NUMA node0 CPU(s): 0-3,16-19
NUMA node1 CPU(s): 4-7,20-23
NUMA node2 CPU(s): 8-11,24-27
NUMA node3 CPU(s): 12-15,28-31
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm arat pln pts md_clear flush_l1d

MemTotal: 528354364 kB

This is my CPU information with RAM
I am using diamond version 2.0.11

And my file size is arround 14GB unzipped.

I am using nr database which is arround 230 GB

So, i got this error
Failed to allocate sufficient memory. Please refer to the manual for instructions on memory usage.

Can anyone help me out on this error.

[GenoMax]

What are you trying to do? Create database or align? You left that information out. DIAMOND can use pre-formatted blast databases now. You should simply go that route.

[Ap1438]

diamond blastx -d /mnt//Diamond/nr -q $path/"$filename"-merged.fastq -o $filename-merged_D.daa -f 100.
Input data is a soil metagenomic data with 150 PE reads. To be used by MEGAN for analysis.

[Peter]

I may be daft, but I dont see how much RAM you actually have?

The simple solution is to use something with more RAM.

[Mensur Dlakic]

Divide the memory in kB by 1024 to get the result in Mb. Then another division by 1024 will get you to Gb.

[Ap1438]

RAM is 512 GB.And its sufficient to run diamond .Because the error is seen after running 1 sample.

[GenoMax]

RAM may be 512G but are you the only person running that DIAMOND jobs on the machine? If this is a shared machine then not all of that 512 may be available or open for DIAMOND.

Answer 1

[Mensur Dlakic]

I try not to point out the obvious as some people consider it insulting, but really:

Please refer to the manual for instructions on memory usage.

Did you consult the manual about this problem?

It would be easy to ask you to get more memory, but it is unlikely that you have another computer around with > 512 Gb. I don't use DIAMOND often, but it seems to me that dividing your input file into parts and doing several searches may give you a better outcome.

[Ap1438]

Thank you for your suggestion. I referred to manual and couldn't find any solution to this problem.But I think dividing the input should help solve the problem.