I am using Humann3 installed via the biobakery conda channel. I am receiving an error when diamond attempts to run. I have tried running fewer threads and receive the same error message. It seems this issue has been raised several times before without a definitive answer. Thank you for your help!
Running diamond …
Aligning to reference database: uniref90_201901b_full.dmnd
CRITICAL ERROR: Error executing: /home/seth2/miniconda3/envs/biobakery/bin/diamond blastx --query /media/seth2/Toshiba/CAZ/trimmed-merged/test7/SRR6897673_trimmed-merged_humann_temp_kzwqs_gn/SRR6897673_trimmed-merged_bowtie2_unaligned.fa --evalue 1.0 --threads 8 --top 1 --outfmt 6 --db /media/seth2/Toshiba/humann_db3/uniref/uniref90_201901b_full --out /media/seth2/Toshiba/CAZ/trimmed-merged/test7/SRR6897673_trimmed-merged_humann_temp_kzwqs_gn/tmp34olbi59/diamond_m8_badq1b99 --tmpdir /media/seth2/Toshiba/CAZ/trimmed-merged/test7/SRR6897673_trimmed-merged_humann_temp_kzwqs_gn/tmp34olbi59
Error message returned from diamond :
diamond v2.0.15.153 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
#CPU threads: 8
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /media/seth2/Toshiba/CAZ/trimmed-merged/test7/SRR6897673_trimmed-merged_humann_temp_kzwqs_gn/tmp34olbi59
Percentage range of top alignment score to report hits: 1
Opening the database… [0.078s]
Database: /media/seth2/Toshiba/humann_db3/uniref/uniref90_201901b_full.dmnd (type: Diamond database, sequences: 87296736, letters: 29247941583)
Block size = 2000000000
Opening the input file… [0.032s]
Opening the output file… [0s]
Loading query sequences… [15.531s]
Masking queries… [16.648s]
Algorithm: Double-indexed
Building query histograms… [11.301s]
Allocating buffers… [0s]
Loading reference sequences… [4.43s]
Masking reference… [11.56s]
Initializing dictionary… [0.016s]
Initializing temporary storage… [0s]
Building reference histograms… [13.15s]
Allocating buffers… [0s]
Processing query block 1, reference block 1/15, shape 1/2, index chunk 1/4.
Building reference seed array… [3.882s]
Building query seed array… [2.453s]
Computing hash join… [2.097s]
Masking low complexity seeds… [0.618s]
Searching alignments… Input/output error
terminate called after throwing an instance of ‘File_write_exception’
what(): Error writing file /media/seth2/Toshiba/CAZ/trimmed-merged/test7/SRR6897673_trimmed-merged_humann_temp_kzwqs_gn/tmp34olbi59/diamond-tmp-dvw9PF