Hello Biobakery Team,
I have installed HUMAnN v4.0.0.alpha.1 following the release notes on Google Docs. Both MetaPhlAn and Bowtie2 work perfectly fine, but I encountered an error when it comes to diamond. I have re-downloaded the UniRef database to ensure the error isn’t related to the database.
Here is the error message:
…
Processing query block 1, reference block 1/1, shape 16/16.
Building reference seed array… [1.535s]
Building query seed array… [0.011s]
Computing hash join… [0.272s]
Searching alignments… [0.912s]
Deallocating memory… [0s]
Deallocating buffers… [0.009s]
Clearing query masking… [0.003s]
Computing alignments…
11/25/2024 05:33:00 PM - humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/home/monash/anaconda3/envs/biobakery4/lib/python3.9/site-packages/humann/utilities.py”, line 761, in execute_command
p_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
File “/home/monash/anaconda3/envs/biobakery4/lib/python3.9/subprocess.py”, line 424, in check_output
File “/home/monash/anaconda3/envs/biobakery4/lib/python3.9/subprocess.py”, line 528, in run
subprocess.CalledProcessError: Command ‘[’/home/monash/anaconda3/envs/biobakery4/bin/diamond’, ‘blastx’, ‘–query’, ‘/mnt/d/tzishin/demo_output/demo_humann_temp/demo_bowtie2_unaligned.fa’, ‘–evalue’, ‘1.0’, ‘–threads’, ‘32’, ‘–top’, ‘1’, ‘–sensitive’, ‘–outfmt’, ‘6’, ‘–db’, ‘/mnt/d/tzishin/humann_db/uniref/humann4_protein_database_filtered_v2019_06’, ‘–out’, ‘/mnt/d/tzishin/demo_output/demo_humann_temp/tmp6gapfbrn/diamond_m8_2ll710fo’, ‘–tmpdir’, ‘/mnt/d/tzishin/demo_output/demo_humann_temp/tmp6gapfbrn’]’ died with <Signals.SIGBUS: 7>.
Here is the code that I used:
humann --input demo.fastq
–input-format fastq
–threads 32
–metaphlan-options “–bowtie2db /mnt/d/tzishin/database/ --index mpa_vOct22_CHOCOPhlAnSGB_202403 --bowtie2out demo_bowtie.sam -o profiled_metagenome.txt -t rel_ab_w_read_stats”
–nucleotide-database /mnt/d/tzishin/humann_db/chocophlan
–protein-database /mnt/d/tzishin/humann_db/uniref
–utility-database /mnt/d/tzishin/humann_db/utility_mapping
–translated-identity-threshold 80.0
–prescreen-threshold 0.01
–output demo_output
–verbose
–memory-use maximum
Thanks in advance for your help!