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Error: the version of diamond in humann3

Hi Francesco,

I try the version of diamond from 0.9.23 to 0.9.32, but some error always showed:

(1) diamond version <= 0.9.23:

(py37) [zhangwenping@localhost try_humann]$ humann --input /data/liying_metagenome/clean_data_liying/SRR5130527_paired.1.fastq --output try_SRR5130527_paired.1 --diamond ‘/data/xmjd/biosoft/’ --metaphlan-options ‘-x mpa_v30_CHOCOPhlAn_201901 --bowtie2db /data/xmjd/miniconda2/envs/py37/lib/python3.7/site-packages/metaphlan/metaphlan_databases/ --read_min_len 49’
Output files will be written to: /data/try_humann/try_SRR5130527_paired.1
Removing spaces from identifiers in input file …

WARNING: Can not call software version for bowtie2

CRITICAL ERROR: Please update diamond from version 0.9.23 to version 0.9.24

(2): diamond version: 0.9.24

07/31/2020 01:48:57 PM - humann.utilities - CRITICAL: Error executing: /data/xmjd/miniconda2/envs/py37/bin/diamond blastx --query /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/SRR5130527_paired.1_bowtie2_unaligned.fa --evalue 1.0 --threads 1 --top 1 --sensitive --outfmt 6 --db /data/xmjd/biobakery_workflows_databases/humann/uniref/uniref90_filtered_201901 --out /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/tmpa6l35xe1/diamond_m8_85rjcnpu --tmpdir /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/tmpa6l35xe1

Error message returned from diamond :
diamond v0.9.24.125 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/tmpa6l35xe1
Opening the database… [0.000337s]
Error: Database was built with a different version of Diamond and is incompatible.

(3) diamond version from 0.9.25 to 0.9.30: same error like the following:

(py37) [zhangwenping@localhost try_humann]$ humann --input /data/liying_metagenome/clean_data_liying/SRR5130527_paired.1.fastq --output try_SRR5130527_paired.1 --diamond ‘/data/xmjd/biosoft/’ --metaphlan-options ‘-x mpa_v30_CHOCOPhlAn_201901 --bowtie2db /data/xmjd/miniconda2/envs/py37/lib/python3.7/site-packages/metaphlan/metaphlan_databases/ --read_min_len 49’
Output files will be written to: /data/try_humann/try_SRR5130527_paired.1
Removing spaces from identifiers in input file …

WARNING: Can not call software version for bowtie2

CRITICAL ERROR: Can not call software version for diamond

(py37) [zhangwenping@localhost try_humann]$ /data/xmjd/biosoft/diamond --version
diamond v0.9.27.128 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

diamond version 0.9.27

(5) diamond version > = 0.9.31:

CRITICAL ERROR: Error executing: /data/xmjd/biosoft/diamond blastx --query /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/SRR5130527_paired.1_bowtie2_unaligned.fa --evalue 1.0 --threads 1 --top 1 --sensitive --outfmt 6 --db /data/xmjd/biobakery_workflows_databases/humann/uniref/uniref90_filtered_201901 --out /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/tmp2318ing3/diamond_m8_gezv43ru --tmpdir /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/tmp2318ing3

Error message returned from diamond :
diamond v0.9.31.132 © Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /data/try_humann/try_SRR5130527_paired.1/SRR5130527_paired.1_humann_temp/tmp2318ing3
Opening the database… [0s]
Error: Database was built with an older version of Diamond and is incompatible.

How can I fix the error?

wenping

1 Like

Can you inspect the database using diamond getseq -d /data/xmjd/biobakery_workflows_databases/humann/uniref/uniref90_filtered_201901 ? Have you by any chance renamed the database file?

Hi, Francesco,

(py37) [zhangwenping@localhost ~] diamond getseq -d /data/xmjd/biobakery_workflows_databases/humann/uniref/uniref90_filtered_201901 Error: Database was built with a different version of Diamond and is incompatible. (py37) [zhangwenping@localhost ~] diamond --version
diamond version 0.9.24
(py37) [zhangwenping@localhost ~] cd /data/xmjd/biobakery_workflows_databases/humann/uniref/ (py37) [zhangwenping@localhost uniref] ls -all
total 49587860
drwxrwxr-x 2 zhangwenping zhangwenping 156 Jul 20 14:52 .
drwxrwxr-x 5 zhangwenping zhangwenping 77 Jul 20 15:04 …
-rw-rw-r-- 1 zhangwenping zhangwenping 12405421206 Jun 12 2019 uniref50_201901.dmnd
-rw-rw-r-- 1 zhangwenping zhangwenping 462767146 Jun 19 2019 uniref50_filtered_201901.dmnd
-rw-rw-r-- 1 zhangwenping zhangwenping 36332007348 Jun 12 2019 uniref90_201901.dmnd
-rw-rw-r-- 1 zhangwenping zhangwenping 1577764898 Jun 19 2019 uniref90_filtered_201901.dmnd
(py37) [zhangwenping@localhost uniref]$

Can you tell me how to fix the error?
wenping

@lauren.j.mciver It seems that the UniRef90 EC filtered database was built using version 0.8. In fact,

diamond-0.8.38/diamond getseq -d uniref90_201901.dmnd | head -n1

>UniRef90_A0A1I2BX06|687 Cluster: CRISPR-associated exonuclease Cas4

MDGDEDYLPLSALQHYLYCPRQCALIHVEQQWAESRHTAEGRVLHEQADKPRGERRRGVRTITALPLAHAGLRLGGIADVVELHDGPDGEQAFPVEYKRGRPKAHRADEVQLCSQALCLEDMLDQPVPQGALFYGATRRRTDVVFDAELRRLTLDTIAATRAMLDAGITPTAEYSARRCDACSLIDLCQPRLLQRRTGVNAWLARQLKSDRNDNGNHEGGEERGTCDGN

@wenping in the meantime, you could extract all the db sequences using diamond 0.8.x and rebuild the database with version 0.9.24

Hi Francesco,

Thank you very much for your help. I found uniref90_filtered_201901.dmnd builted with diamond 0.8.38 and rebuilt the database with version 0.9.24. It works.

wenping

Hi @fbeghini, Thank you for the catch and ping. I can confirm the UniRef90 EC filtered database v201901 is formatted for diamond v0.8.22 (the prior diamond that we had been using, db version 0) and it does not work with the newer diamond v0.9.24 (db version 2). I checked the UniRef50 EC filtered database v201901 and it looks like it is compatible with diamond v0.9.24 (db version 2). I have rebuilt and posted the UniRef90 filtered database v201901 with diamond v0.9.24.

Hi @wenping, Thank you for your post and sorry for the confusion. Thank you for rebuilding the database on your own. The updated database (with diamond v0.9.24) has been posted so others should not come across the same error.

Thank you,
Lauren

Hi Lauren,

While running humann3 I am getting following error.
CRITICAL ERROR: Please update diamond from version 0.9.24 to version 0.9.36

I have checked the uniref database and it says database was built with different version of diamond
diamond getseq -d uniref90_201901b_full.dmnd

Error: Database was built with a different version of Diamond and is incompatible.

I have installed latest version of humann3
conda activate biobakery3
conda install humann -c biobakery

Can you please suggest how to update diamond version.

1 Like

Edit: Solved the problem by conda install -c bioconda diamond=0.9.36

I also recently tried to run humann3 with the same error here after installing using these direction. Here is the log file:

06/10/2021 02:44:43 PM - humann.humann - INFO: Running humann v3.0.0
06/10/2021 02:44:43 PM - humann.humann - INFO: Output files will be written to: /dfs/ROOTS/Myrold_Lab/Chris/dirt/humann/NI-19-A
06/10/2021 02:44:43 PM - humann.humann - INFO: Writing temp files to directory: /dfs/ROOTS/Myrold_Lab/Chris/dirt/humann/NI-19-A/NI-19-A_filtered_humann_temp
06/10/2021 02:44:43 PM - humann.utilities - INFO: File ( /dfs/ROOTS/Myrold_Lab/Chris/dirt/filtered/NI-19-A_filtered.fastq.gz ) is of format:  fastq.gz
06/10/2021 02:44:43 PM - humann.utilities - INFO: Decompressing gzipped file ...
06/10/2021 02:56:32 PM - humann.humann - INFO: Removing spaces from identifiers in input file
06/10/2021 03:13:34 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
06/10/2021 03:13:35 PM - humann.utilities - INFO: Using metaphlan version 3.0
06/10/2021 03:13:35 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
06/10/2021 03:13:35 PM - humann.utilities - WARNING: Can not call software version for bowtie2
06/10/2021 03:13:35 PM - humann.utilities - INFO: Using bowtie2 version UNK
06/10/2021 03:13:35 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
06/10/2021 03:13:35 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.36
06/10/2021 03:13:35 PM - humann.utilities - CRITICAL: Please update diamond from version 0.9.24 to version 0.9.36
1 Like

Hi @cjburgess , Thank you for the post.

Hi @ashoks773 , Sorry for my slow response. Please post again if you are still having issues.

Thank you both,
Lauren

Thanks! It really helped