Error: Unexpected end of input.

Microbial community profiling HUMAnN
1

Database: /Users/arrow/HumannDB/uniref//uniref90_201901b_full.dmnd (type: Diamond database, sequences: 87296736, letters: 29247941583)
Block size = 2000000000
Opening the input file… [0.152s]
Opening the output file… [0s]
Loading query sequences… [7.507s]
Masking queries… [47.923s]
Algorithm: Double-indexed
Building query histograms… [13.441s]
Allocating buffers… [0.001s]
Loading reference sequences… [0.003s]
Error: Unexpected end of input.

05/25/2022 02:44:48 PM - humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/usr/local/lib/python3.9/site-packages/humann/utilities.py”, line 756, in execute_command
p_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
File “/usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py”, line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File “/usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py”, line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command ‘[’/opt/miniconda3/bin/diamond’, ‘blastx’, ‘–query’, ‘/Volumes/PabloSSD/HUMMAN2/DEC/Sequences/10.1/10_S16.R1_kneaddata_paired_1_humann_temp/10_S16.R1_kneaddata_paired_1_bowtie2_unaligned.fa’, ‘–evalue’, ‘1.0’, ‘–threads’, ‘1’, ‘–top’, ‘1’, ‘–outfmt’, ‘6’, ‘–db’, ‘/Users/arrow/HumannDB/uniref//uniref90_201901b_full’, ‘–out’, ‘/Volumes/PabloSSD/HUMMAN2/DEC/Sequences/10.1/10_S16.R1_kneaddata_paired_1_humann_temp/tmp1iuk1v2q/diamond_m8_iia6qsqv’, ‘–tmpdir’, ‘/Volumes/PabloSSD/HUMMAN2/DEC/Sequences/10.1/10_S16.R1_kneaddata_paired_1_humann_temp/tmp1iuk1v2q’]’ returned non-zero exit status 1.

05/25/2022 02:44:48 PM - humann.utilities - INFO: Total memory = 8.0 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Available memory = 0.8191642761230469 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Free memory = 0.5248031616210938 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Percent memory used = 89.8 %
05/25/2022 02:44:48 PM - humann.utilities - INFO: CPU percent = 0.0 %
05/25/2022 02:44:48 PM - humann.utilities - INFO: Total cores count = 8
05/25/2022 02:44:48 PM - humann.utilities - INFO: Total disk = 460.4317207336426 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Used disk = 322.24969482421875 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Percent disk used = 70.0 %
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process create time = 2022-05-25 14:01:50
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process user time = 9.68513024 seconds
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process system time = 0.305115904 seconds
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process CPU percent = 0.5 %
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process memory RSS = 0.013401031494140625 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process memory VMS = 37.89091491699219 GB
05/25/2022 02:44:48 PM - humann.utilities - INFO: Process memory percent = 0.16884803771972656 %

2

Sorry for the slow reply. A similar error was reported recently in the thread below. I will try to work the problem there. Feel free to add additional details about your situation there if helpful.