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
Please cite: Sensitive protein alignments at tree-of-life scale using DIAMOND | Nature Methods 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 <Signals.SIGILL: 4>.
#The end