The bioBakery help forum

HUMAnN3 Diamond tmp file doesnt exist

For only a couple of my samples, I got two error messages when Diamond was running. It seems that it cannot save the joined output blocks to the diamond tmp directory because the directory doesn’t exist. Should I simply create the directory and resume humann?

First:

06/10/2020 05:27:39 AM - humann.utilities - CRITICAL: Error executing: /home/CSCScience.ca/amirza/miniconda3/envs/biobakery3/bin/diamond blastx --query /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/HSC-10099-HC-01_S8_bowtie2_unaligned.fa --evalue 1.0 --threads 8 --top 1 --outfmt 6 --db /home/CSCScience.ca/amirza/biobakery_databases/humann2/uniref/uniref90_201901 --out /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/tmpap8y90uh/diamond_m8_2_azlphp --tmpdir /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/tmpap8y90uh

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.

Then Diamond runs and fails to join output blocks:

Building seed filter...  [0.611389s]
Searching alignments...  [44.898s]
Deallocating buffers...  [0.033879s]
Opening temporary output file...  [0.076705s]
Computing alignments...  [63.8764s]
Deallocating reference...  [0.009413s]
Loading reference sequences...  [0.041094s]
Deallocating buffers...  [0.015319s]
Joining output blocks... Bad file descriptor
 [0.005746s]
Error: Error writing file /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/tmpap8y90uh/diamond-tmp-85U4Ua

06/10/2020 05:27:39 AM - humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery3/lib/python3.7/site-packages/humann/utilities.py", line 734, in execute_command
    p_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery3/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery3/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/home/CSCScience.ca/amirza/miniconda3/envs/biobakery3/bin/diamond', 'blastx', '--query', '/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/HSC-10099-HC-01_S8_bowtie2_unaligned.fa', '--evalue', '1.0', '--threads', '8', '--top', '1', '--outfmt', '6', '--db', '/home/CSCScience.ca/amirza/biobakery_databases/humann2/uniref/uniref90_201901', '--out', '/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/tmpap8y90uh/diamond_m8_2_azlphp', '--tmpdir', '/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery/humann3/main-2/HSC-10099-HC-01_S8_humann_temp/tmpap8y90uh']' returned non-zero exit status 1.

Sorry for the delay - I haven’t seen this before. It looks like it might be a problem with reading/writing to the disk you’re working with.

Simply starting over solved the problem.