Error running diamond: Error: Invalid output field: scovhsp

[gdefazio]

Hi there,

I'm running emapper but the following error has been raised during the execution:

#  emapper-2.1.3
# emapper.py  --cpu 32 -i /lustrehome/gdefazio/onehealth/sequenziamento_vero/drep/annotation_on_drep/LMT0_A_S4_bin.101.fa.faa -o /lustrehome/gdefazio/onehealth/sequenziamento_vero/drep/eggnog_on_drep/LMT0_A_S4_bin.101.fa.faa
ESC[1;33m  /lustrehome/gdefazio/miniconda3/envs/eggnog/bin/diamond blastp -d /lustrehome/gdefazio/miniconda3/envs/eggnog/lib/python3.13/site-packages/data/eggnog_proteins.dmnd -q /lustrehome/gdefazio/onehealth/sequenziamento_vero/drep/annotation_on_drep/LMT0_A_S4_bin.101.fa.faa --threads 32 -o /lustrehome/gdefazio/onehealth/sequenziamento_vero/drep/eggnog_on_drep/LMT0_A_S4_bin.101.fa.faa.emapper.hits  --sensitive -e 0.001 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhspESC[0m
Error running diamond: Error: Invalid output field: scovhsp

This is the conda list output for the eggnog-mapper conda env:

 # packages in environment at /lustrehome/gdefazio/miniconda3/envs/eggnog:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
biopython                 1.85            py313hb25bd0a_0  
blas                      1.0                         mkl  
bzip2                     1.0.8                h5eee18b_6  
ca-certificates           2025.9.9             h06a4308_0  
diamond                   0.9.19               h2e03b76_5    bioconda
easel                     0.48                 hec16e2b_1    bioconda
eggnog-mapper             2.1.3              pyhdfd78af_0    bioconda
expat                     2.7.1                h6a678d5_0  
gawk                      5.3.1                h5eee18b_0  
gettext                   0.21.0               hedfda30_2  
hmmer                     3.3.2                h87f3376_2    bioconda
icu                       73.1                 h6a678d5_0  
intel-openmp              2025.0.0          h06a4308_1171  
ld_impl_linux-64          2.44                 h153f514_2  
libffi                    3.4.4                h6a678d5_1  
libgcc-ng                 11.2.0               h1234567_1  
libgomp                   11.2.0               h1234567_1  
libiconv                  1.16                 h5eee18b_3  
libidn2                   2.3.8                hf80d704_0  
libmpdec                  4.0.0                h5eee18b_0  
libstdcxx-ng              11.2.0               h1234567_1  
libunistring              1.3                  hb25bd0a_0  
libuuid                   1.41.5               h5eee18b_0  
libxcb                    1.17.0               h9b100fa_0  
libxml2                   2.13.8               hfdd30dd_0  
mkl                       2025.0.0           hacee8c2_941  
mkl-service               2.5.2           py313hacdc0fc_0  
mkl_fft                   2.1.1           py313h57662e1_0  
mkl_random                1.3.0           py313h23c847b_0  
mmseqs2                   13.45111             h95f258a_1    bioconda
ncurses                   6.5                  h7934f7d_0  
numpy                     2.3.3           py313h720eef7_1  
numpy-base                2.3.3           py313h95072fd_1  
openssl                   3.0.18               hd6dcaed_0  
pcre2                     10.46                hf426167_0  
pip                       25.2               pyhc872135_1  
prodigal                  2.6.3                hec16e2b_4    bioconda
psutil                    7.0.0           py313hee96239_0  
pthread-stubs             0.3                  h0ce48e5_1  
python                    3.13.9          h7e8bc2b_100_cp313  
python_abi                3.13                    1_cp313  
readline                  8.3                  hc2a1206_0  
setuptools                80.9.0          py313h06a4308_0  
sqlite                    3.50.2               hb25bd0a_1  
tbb                       2022.0.0             hdb19cb5_0  
tbb-devel                 2022.0.0             hdb19cb5_0  
tk                        8.6.15               h54e0aa7_0  
tzdata                    2025b                h04d1e81_0  
wget                      1.25.0               he4200e1_2  
wheel                     0.45.1          py313h06a4308_0  
xorg-libx11               1.8.12               h9b100fa_1  
xorg-libxau               1.0.12               h9b100fa_0  
xorg-libxdmcp             1.1.5                h9b100fa_0  
xorg-xorgproto            2024.1               h5eee18b_1  
xz                        5.6.4                h5eee18b_1  
zlib                      1.2.13               hd233ad5_2 

Please let me know how this error can be fixed.

[bbuchfink]

Your diamond version is way too old, and does not support this feature. Update it manually if needed. I strongly recommend to always use the latest version.

@eggnogdb It is better to abort with an error if outdated software versions are used.