# Diamond (v2.1.8) reported a fatal error when running humann (v3.8) **URL:** \ **Category:** HUMAnN\ **Created:** [November 30, 2023, 1:25pm UTC](https://forum.biobakery.org/t/diamond-v2-1-8-reported-a-fatal-error-when-running-humann-v3-8/6269 "2023-11-30T13:25:13Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Zhangtao](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/zhangtao/32/2462_2.png) [@Zhangtao](https://forum.biobakery.org/u/Zhangtao)\ **Post date:** [November 30, 2023, 1:25pm UTC](https://forum.biobakery.org/t/diamond-v2-1-8-reported-a-fatal-error-when-running-humann-v3-8/6269/1 "2023-11-30T13:25:13Z")
Dear developers, When I used the command “humann --input A1.fastq --output A1 --threads 20 --metaphlan-options “–index mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --bowtie2db /home/data/t150431/miniconda3/envs/metaphlan/lib/python3.10/site-packages/metaphlan/metaphlan\_databases” --memory-use maximum” to perform functional analysis, diamond software showed a fatal error. Although I have seen similar problems in the forum, I have still not found a solution. One clue is that when I add “–bypass-translated-search” to the above command, the humann can complete the task normally. Any help or tips would be much appreciated! Yours faithfully, Tao Zhang #A1.log 11/30/2023 09:42:36 AM - humann.search.translated - INFO: Running diamond … 11/30/2023 09:42:36 AM - humann.search.translated - INFO: Aligning to reference database: uniref90\_201901b\_full.dmnd 11/30/2023 09:42:36 AM - humann.utilities - DEBUG: Remove file: /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x/diamond\_m8\_lo5b3ju9 11/30/2023 09:42:36 AM - humann.utilities - DEBUG: Using software: /home/data/t150431/miniconda3/envs/biobakery3/bin/diamond 11/30/2023 09:42:36 AM - humann.utilities - INFO: Execute command: /home/data/t150431/miniconda3/envs/biobakery3/bin/diamond blastx --query /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/A1\_bowtie2\_unaligned.fa --evalue 1.0 --threads 20 --top 1 --outfmt 6 --db /home/data/t150431/humann\_database/UniRef\_database/uniref90\_201901b\_full --out /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x/diamond\_m8\_lo5b3ju9 --tmpdir /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x 11/30/2023 09:43:05 AM - humann.utilities - CRITICAL: Error executing: /home/data/t150431/miniconda3/envs/biobakery3/bin/diamond blastx --query /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/A1\_bowtie2\_unaligned.fa --evalue 1.0 --threads 20 --top 1 --outfmt 6 --db /home/data/t150431/humann\_database/UniRef\_database/uniref90\_201901b\_full --out /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x/diamond\_m8\_lo5b3ju9 --tmpdir /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x Error message returned from diamond : diamond v2.1.8.162 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at [http://www.diamondsearch.org](http://www.diamondsearch.org) Please cite: [Sensitive protein alignments at tree-of-life scale using DIAMOND | Nature Methods](http://dx.doi.org/10.1038/s41592-021-01101-x) Nature Methods (2021) #CPU threads: 20 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Temporary directory: /home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x Percentage range of top alignment score to report hits: 1 Opening the database… [0.414s] Database: /home/data/t150431/humann\_database/UniRef\_database/uniref90\_201901b\_full (type: Diamond database, sequences: 87296736, letters: 29247941583) Block size = 2000000000 Opening the input file… [0.112s] Opening the output file… [0s] Loading query sequences… [27.796s] Masking queries… 11/30/2023 09:43:05 AM - humann.utilities - CRITICAL: TRACEBACK: Traceback (most recent call last): File “/home/data/t150431/miniconda3/envs/biobakery3/lib/python3.10/site-packages/humann/utilities.py”, line 761, in execute\_command p\_out = subprocess.check\_output(cmd, stderr=subprocess.STDOUT) File “/home/data/t150431/miniconda3/envs/biobakery3/lib/python3.10/subprocess.py”, line 421, in check\_output return run(\*popenargs, stdout=PIPE, timeout=timeout, check=True, File “/home/data/t150431/miniconda3/envs/biobakery3/lib/python3.10/subprocess.py”, line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command ‘[’/home/data/t150431/miniconda3/envs/biobakery3/bin/diamond’, ‘blastx’, ‘–query’, ‘/home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/A1\_bowtie2\_unaligned.fa’, ‘–evalue’, ‘1.0’, ‘–threads’, ‘20’, ‘–top’, ‘1’, ‘–outfmt’, ‘6’, ‘–db’, ‘/home/data/t150431/humann\_database/UniRef\_database/uniref90\_201901b\_full’, ‘–out’, ‘/home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x/diamond\_m8\_lo5b3ju9’, ‘–tmpdir’, ‘/home/data/t150431/test/clean\_data/A1\_1/A1\_humann\_temp/tmpzi8t1k6x’]’ died with \. #The end ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [December 8, 2023, 7:38pm UTC](https://forum.biobakery.org/t/diamond-v2-1-8-reported-a-fatal-error-when-running-humann-v3-8/6269/2 "2023-12-08T19:38:34Z")
That definitely indicates a problem during translated search. Is it possible you’re running out of memory? You could also try downgrading your DIAMOND version. I tested HUMAnN 3.6 against DIAMOND 2.0.15, so I know that pairing works. ---
**Author:** ![Zhangtao](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/zhangtao/32/2462_2.png) [@Zhangtao](https://forum.biobakery.org/u/Zhangtao)\ **Post date:** [December 15, 2023, 10:31am UTC](https://forum.biobakery.org/t/diamond-v2-1-8-reported-a-fatal-error-when-running-humann-v3-8/6269/3 "2023-12-15T10:31:47Z")
Thank you. I’ll wait for HUMAnN 4.