Diamond version Error: HUMANn3

Microbial community profiling HUMAnN
1

Hello,
I tried to run the humann3, but I faced to diamond version error.
Can anyone please tell how to solve those error?

(metaphlan) tbd01188@pc102-X399-AORUS-XTREME:/media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned$ …/…/./humann3.sh
Output files will be written to: /media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned/humann

Writing temp files to directory: /media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned/humann/AD1output-trim_humann_temp_k1_7td9j

File ( /media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned/AD1output-trim.fastq ) is of format: fastq

Removing spaces from identifiers in input file …

CRITICAL ERROR: Please update diamond from version 0.9.24 to version 0.9.36

Output files will be written to: /media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned/humann

Writing temp files to directory: /media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned/humann/AD2output-trim_humann_temp_zl5cwuhv

File ( /media/hdd/14Tb_1/tbd01188_backup/DGU/raw_data/bowtie_unaligned/AD2output-trim.fastq ) is of format: fastq

Removing spaces from identifiers in input file …

Thanks,
MinJi

2

Hi MinJi,

I had same error, solved by updating diamond:

conda install -c bioconda diamond=0.9.36

check to see if version is correct

diamond --version

2 Likes
3

Hi @aemann01 ! I currently did the same thing to update diamond. I tried to run humann with the updated diamond version (within biobakery workflow), but my analysis with test data was stuck in limbo. Did you have any problems running your analysis after the update?

4

@bmtalbot it took a long while to complete the diamond alignment step using one thread on my machine but eventually finished (took me ~1hr 30min with 4 threads). Do you know what step you’re stalling on? You can check which step is currently running by looking at the end of the demo.log file.