Diamond Error Invalid DAA file

[Kinya Beth]

ello Humann2 users

I am running humann2 on my fastq files and keep getting these error at the diamond step. Am using the current version of humann2 and my shell script is: 

humann2 --input /users/so/bmutai/metasub/MS006_14506_ACAGTG_read1.fastq --input-format fastq --metaphlan /users/so/bmutai/biobakery-metaphlan2-e82c52bf0f42/ --nucleotide-database /users/so/bmutai/chocophlan/chocophlan/ --protein-database /users/so/bmutai/uniref/uniref/ --output /users/so/bmutai/metasub/

Total gene families from nucleotide alignment: 40515

Unaligned reads after nucleotide alignment: 97.1279158262 %

Running diamond ........

Aligning to reference database: uniref90.ec_filtered.dmnd

CRITICAL ERROR: Error executing: /users/so/bmutai/utils/anaconda2/bin/diamond view --threads 1 --daa /users/so/bmutai/metasub/MS002_14506_CGATGT_read1_humann2_temp/tmpB2h8IB/diamond_daa_GS5KVF.daa --out /users/so/bmutai/metasub/MS002_14506_CGATGT_read1_humann2_temp/tmpB2h8IB/diamond_m8_Jon1QD

Error message returned from diamond :

Error: Invalid DAA file. DIAMOND run probably has not completed successfully.

I will appreciate any help.

Thank you 

[Lauren McIver]

Hello Kinya,

It looks like you might be running out of memory during the diamond step. How much memory is available on your machine? If you have the python package psutil installed, humann2 will print out disk space and memory use stats to the log file if there is an error running a subprocess to help with debugging.

Thanks!

Lauren

[Kinya Beth]

Hi Lauren. Thank you. Increasing the memory solved the problem.