I was trying to run humann3 in an anaconda3 environment on my institution’s computing cluster (using a SLURM workload manager and script) when I ran into this error:
humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/home/azahorik/.conda/envs/biobakery3/lib/python3.7/site-packages/humann/utilities.py”, line 761, in execute_command
p_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
File “/home/azahorik/.conda/envs/biobakery3/lib/python3.7/subprocess.py”, line 411, in check_output
**kwargs).stdout
File “/home/azahorik/.conda/envs/biobakery3/lib/python3.7/subprocess.py”, line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[’/home/azahorik/.conda/envs/biobakery3/bin/diamond’, ‘blastx’, ‘–query’, ‘/work/azahorik/oyster/data/humann3_results/Trinity-coassembly_humann_temp/tmpuze92gj4/tmpn9ayg_ll’, ‘–evalue’, ‘1.0’, ‘–threads’, ‘1’, ‘–top’, ‘1’, ‘–outfmt’, ‘6’, ‘–db’, ‘/work/azahorik/oyster/data/humann_dbs/uniref/uniref90_201901b_full’, ‘–out’, ‘/work/azahorik/oyster/data/humann3_results/Trinity-coassembly_humann_temp/tmpuze92gj4/diamond_m8_q75zz8ze’, ‘–tmpdir’, ‘/work/azahorik/oyster/data/humann3_results/Trinity-coassembly_humann_temp/tmpuze92gj4’]’ returned non-zero exit status 1.
I’m honestly a bit of a bioinformatics novice, so any help pinning down what went wrong and how to fix it would be appreciated! I did some Googling and searched the forum, but couldn’t find mention of an analogous error.
Thanks!
e: I checked my slurm output, and found this as well:
Loading reference sequences… Stale file handle [0s]
Error: Error reading file /work/azahorik/oyster/data/humann_dbs/uniref/uniref90_201901b_full.dmnd