[barrnap] ERROR: nhmmer failed to run

[nick-youngblut]

I'm getting the following error:

[barrnap] This is barrnap 0.9
[barrnap] Written by Torsten Seemann
[barrnap] Obtained from https://github.com/tseemann/barrnap
[barrnap] Detected operating system: linux
[barrnap] Adding /ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/lib/barrnap/bin/../binaries/linux to end of PATH
[barrnap] Checking for dependencies:
[barrnap] Found nhmmer - /ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/bin/nhmmer
[barrnap] Found bedtools - /ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/bin/bedtools
[barrnap] Will use 4 threads
[barrnap] Setting evalue cutoff to 1e-06
[barrnap] Will tag genes < 0.8 of expected length.
[barrnap] Will reject genes < 0.25 of expected length.
[barrnap] Using database: /ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/lib/barrnap/bin/../db/bac.hmm
[barrnap] Scanning /ebio/abt3_scratch/nyoungblut/LLG_8797531528/genomes/X361_fail_Common_Opossum__maxbin2__High.001.fna for bac rRNA genes... please wait
[barrnap] Command: nhmmer --cpu 4 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/lib/barrnap/bin/../db/bac.hmm' '/ebio/abt3_scratch/nyoungblut/LLG_8797531528/genomes/X361_fail_Common_Opossum__maxbin2__High.001.fna'
[barrnap] ERROR: nhmmer failed to run - # Target file:     /ebio/abt3_scratch/nyoungblut/LLG_8797531528/genomes/X361_fail_Common_Opossum__maxbin2__High.001.fna

However, when I activate that conda env and run nhmmer myself, the run completes successfully:

$ nhmmer --cpu 4 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/lib/barrnap/bin/../db/bac.hmm' '/ebio/abt3_scratch/nyoungblut/LLG_8797531528/genomes/X361_fail_Common_Opossum__maxbin2__High.001.fna' || echo "ERROR!"
# target name        accession  query name           accession  hmmfrom hmm to alifrom  ali to envfrom  env to  sq len strand   E-value  score  bias  description of target
#------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- ---------------------
#
# Program:         nhmmer
# Version:         3.1b2 (February 2015)
# Pipeline mode:   SEARCH
# Query file:      /ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/lib/barrnap/bin/../db/bac.hmm
# Target file:     /ebio/abt3_scratch/nyoungblut/LLG_8797531528/genomes/X361_fail_Common_Opossum__maxbin2__High.001.fna
# Option settings: nhmmer -o /dev/null --tblout /dev/stdout -E 1e-06 --w_length 3878 --cpu 4 /ebio/abt3_projects/Georg_animal_feces/bin/llg/.snakemake/conda/6db1e2f9/lib/barrnap/bin/../db/bac.hmm /ebio/abt3_scratch/nyoungblut/LLG_8797531528/genomes/X361_fail_Common_Opossum__maxbin2__High.001.fna
# Current dir:     /ebio/abt3_projects/Georg_animal_feces/bin/llmga
# Date:            Fri Jan 29 09:11:22 2021
# [ok]

The input genome fasta file contains 123 contigs, and it is a valid fasta file.

My conda env:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.1.5             h516909a_1002    conda-forge
arb-bio-tools             6.0.6                haa8b8d8_8    bioconda
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
barrnap                   0.9                           2    bioconda
bedtools                  2.29.2               hc088bd4_0    bioconda
bibtexparser              1.1.0                      py_0    conda-forge
binutils_impl_linux-64    2.33.1               h53a641e_8    conda-forge
binutils_linux-64         2.33.1              h9595d00_17    conda-forge
bioconductor-biobase      2.42.0           r351h14c3975_1    bioconda
bioconductor-biocgenerics 0.28.0                   r351_1    bioconda
bioconductor-biocparallel 1.16.6           r351h1c2f66e_0    bioconda
bioconductor-biostrings   2.50.2           r351h14c3975_0    bioconda
bioconductor-dada2        1.10.0           r351hf484d3e_0    bioconda
bioconductor-delayedarray 0.8.0            r351h14c3975_0    bioconda
bioconductor-genomeinfodb 1.18.1                   r351_0    bioconda
bioconductor-genomeinfodbdata 1.2.1                    r351_0    bioconda
bioconductor-genomicalignments 1.18.1           r351h14c3975_0    bioconda
bioconductor-genomicranges 1.34.0           r351h14c3975_0    bioconda
bioconductor-iranges      2.16.0           r351h14c3975_0    bioconda
bioconductor-rsamtools    1.34.0           r351hf484d3e_0    bioconda
bioconductor-s4vectors    0.20.1           r351h14c3975_0    bioconda
bioconductor-shortread    1.40.0           r351hf484d3e_0    bioconda
bioconductor-summarizedexperiment 1.12.0                   r351_0    bioconda
bioconductor-xvector      0.22.0           r351h14c3975_0    bioconda
bioconductor-zlibbioc     1.28.0           r351h14c3975_0    bioconda
biom-format               2.1.8            py36ha112f06_1    conda-forge
blas                      2.14                   openblas    conda-forge
blast                     2.9.0           pl526h3066fca_4    bioconda
bleach                    3.1.1                      py_0    conda-forge
bokeh                     1.4.0            py36h9f0ad1d_1    conda-forge
boost                     1.68.0          py36h8619c78_1001    conda-forge
boost-cpp                 1.68.0            h11c811c_1000    conda-forge
bwidget                   1.9.14                        0    conda-forge
bzip2                     1.0.8                h516909a_3    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
cachecontrol              0.12.5                     py_0    conda-forge
cairo                     1.16.0            h18b612c_1001    conda-forge
certifi                   2019.11.28       py36h9f0ad1d_1    conda-forge
cffi                      1.13.2           py36h8022711_0    conda-forge
chardet                   3.0.4           py36h9880bd3_1008    conda-forge
click                     7.0                        py_0    conda-forge
cryptography              2.8              py36h45558ae_2    conda-forge
curl                      7.68.0               hf8cf82a_0    conda-forge
cutadapt                  2.8              py36h516909a_0    bioconda
cycler                    0.10.0                   py36_0    conda-forge
cython                    0.29.15          py36h831f99a_1    conda-forge
dbus                      1.13.6               he372182_0    conda-forge
deblur                    1.1.0                    py36_0    bioconda
decorator                 4.4.1                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
dendropy                  4.4.0              pyh864c0ab_2    bioconda
dnaio                     0.4.1            py36h516909a_0    bioconda
emperor                   1.0.0                    py36_0    conda-forge
entrez-direct             13.9            pl526h375a9b1_0    bioconda
entrypoints               0.3             py36h9f0ad1d_1002    conda-forge
expat                     2.2.9                he1b5a44_2    conda-forge
fastcluster               1.1.26           py36h7c3b610_2    conda-forge
fasttree                  2.1.10                        0    bioconda
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.0               he06d7ca_2    conda-forge
future                    0.18.2           py36h5fab9bb_3    conda-forge
gcc_impl_linux-64         7.3.0                hd420e75_5    conda-forge
gcc_linux-64              7.3.0               h553295d_17    conda-forge
gettext                   0.19.8.1          hf34092f_1004    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_5    conda-forge
gfortran_linux-64         7.3.0               h553295d_17    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.58.3          py36hd3ed26a_1004    conda-forge
gmp                       6.2.0                h58526e2_4    conda-forge
gneiss                    0.4.6                      py_0    bioconda
gnutls                    3.6.5             hd3a4fd2_1002    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
gst-plugins-base          1.14.5               h0935bb2_2    conda-forge
gstreamer                 1.14.5               h36ae1b5_2    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_5    conda-forge
gxx_linux-64              7.3.0               h553295d_17    conda-forge
h5py                      2.10.0          nompi_py36h513d04c_102    conda-forge
harfbuzz                  2.4.0                h37c48d4_1    conda-forge
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
hdmedians                 0.13            py36h785e9b2_1002    conda-forge
hmmer                     3.1b2                         3    bioconda
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.9                      py36_0    conda-forge
ijson                     2.6.1                      py_0    conda-forge
importlib_metadata        1.5.0                    py36_0    conda-forge
ipykernel                 5.1.4            py36h5ca1d4c_0    conda-forge
ipython                   7.12.0           py36h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                    py36_0    conda-forge
ipywidgets                7.5.1              pyh9f0ad1d_1    conda-forge
iqtree                    1.6.12               he513fc3_1    bioconda
jedi                      0.16.0           py36h9f0ad1d_1    conda-forge
jinja2                    2.11.1                     py_0    conda-forge
joblib                    0.14.1             pyh9f0ad1d_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.2.0            py36h9f0ad1d_1    conda-forge
jupyter_client            6.0.0                      py_0    conda-forge
jupyter_core              4.6.3            py36h9f0ad1d_2    conda-forge
kiwisolver                1.1.0            py36hdb11119_1    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
lcms2                     2.9                  hbd6801e_2    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_8    conda-forge
libarbdb                  6.0.6                haa8b8d8_8    bioconda
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libcurl                   7.68.0               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
liblapacke                3.8.0               14_openblas    conda-forge
libopenblas               0.3.7                h5ec1e0e_6    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.9                h13577e0_2    conda-forge
lockfile                  0.12.2                   py36_0    conda-forge
lz4-c                     1.8.3             hf484d3e_1001    conda-forge
mafft                     7.310                he1b5a44_3    bioconda
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                1.1.1            py36he6145b8_2    conda-forge
matplotlib                3.1.1                    py36_0    conda-forge
matplotlib-base           3.1.1            py36hfd891ef_0    conda-forge
mistune                   0.8.4           py36h8c4c3a4_1002    conda-forge
more-itertools            8.2.0                      py_1    conda-forge
msgpack-python            1.0.0            py36hdb11119_2    conda-forge
natsort                   7.0.1                      py_0    conda-forge
nbconvert                 5.6.1            py36h9f0ad1d_1    conda-forge
nbformat                  5.0.4                      py_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
nettle                    3.4.1             h14c3975_1002    conda-forge
networkx                  2.4                        py_1    conda-forge
nose                      1.3.7           py36h9f0ad1d_1004    conda-forge
notebook                  6.0.3            py36h9f0ad1d_1    conda-forge
numpy                     1.18.1           py36h7314795_1    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjdk                   11.0.1            h600c080_1018    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
packaging                 20.1                       py_0    conda-forge
pandas                    0.25.3           py36hb3f55d8_0    conda-forge
pandoc                    2.9.2.1                       0    conda-forge
pandocfilters             1.4.2                    py36_0    conda-forge
pango                     1.40.14           he7ab937_1005    conda-forge
parso                     0.6.1                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.26.2            h36c2ea0_1008    conda-forge
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-archive-tar          2.32                    pl526_0    bioconda
perl-base                 2.23                    pl526_1    bioconda
perl-business-isbn        3.004                   pl526_0    bioconda
perl-business-isbn-data   20140910.003            pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-bzip2   2.087           pl526he1b5a44_0    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-digest-hmac          1.03                    pl526_3    bioconda
perl-digest-md5           2.55                    pl526_0    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-encode-locale        1.05                    pl526_6    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-listing         6.04                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-html-parser          3.72            pl526h6bb024c_5    bioconda
perl-html-tagset          3.20                    pl526_3    bioconda
perl-html-tree            5.07                    pl526_1    bioconda
perl-http-cookies         6.04                    pl526_0    bioconda
perl-http-daemon          6.01                    pl526_1    bioconda
perl-http-date            6.02                    pl526_3    bioconda
perl-http-message         6.18                    pl526_0    bioconda
perl-http-negotiate       6.01                    pl526_3    bioconda
perl-io-compress          2.087           pl526he1b5a44_0    bioconda
perl-io-html              1.001                   pl526_2    bioconda
perl-io-socket-ssl        2.066                   pl526_0    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-libwww-perl          6.39                    pl526_0    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-lwp-mediatypes       6.04                    pl526_0    bioconda
perl-lwp-protocol-https   6.07                    pl526_4    bioconda
perl-mime-base64          3.15                    pl526_1    bioconda
perl-mozilla-ca           20180117                pl526_1    bioconda
perl-net-http             6.19                    pl526_0    bioconda
perl-net-ssleay           1.88            pl526h90d6eec_0    bioconda
perl-ntlm                 1.09                    pl526_4    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-socket               2.027                   pl526_1    bioconda
perl-storable             3.15            pl526h14c3975_0    bioconda
perl-test-requiresinternet 0.05                    pl526_0    bioconda
perl-time-local           1.28                    pl526_1    bioconda
perl-try-tiny             0.30                    pl526_1    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-uri                  1.76                    pl526_0    bioconda
perl-www-robotrules       6.02                    pl526_3    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44_01         pl526ha1d75be_1002    conda-forge
perl-xml-sax              1.02                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_3    bioconda
perl-xml-simple           2.25                    pl526_1    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
pexpect                   4.8.0            py36h9f0ad1d_1    conda-forge
pickleshare               0.7.5           py36h9f0ad1d_1002    conda-forge
pigz                      2.3.4                hed695b0_1    conda-forge
pillow                    7.0.0            py36h8328e55_1    conda-forge
pip                       20.0.2                   py36_1    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pluggy                    0.12.0                     py_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            3.0.3                      py_0    conda-forge
psutil                    5.7.0            py36h8c4c3a4_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
py                        1.8.1                      py_0    conda-forge
pycparser                 2.19                     py36_1    conda-forge
pygments                  2.5.2                      py_0    conda-forge
pyopenssl                 19.1.0                   py36_0    conda-forge
pyparsing                 2.4.6                      py_0    conda-forge
pyqt                      5.9.2            py36hcca6a23_4    conda-forge
pyrsistent                0.15.7           py36h8c4c3a4_1    conda-forge
pysocks                   1.7.1            py36h5fab9bb_3    conda-forge
pytest                    5.3.5            py36h9f0ad1d_2    conda-forge
python                    3.6.7           h357f687_1008_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
pytz                      2019.3                     py_0    conda-forge
pyyaml                    5.3.1            py36h8c4c3a4_0    conda-forge
pyzmq                     19.0.0           py36h9947dbf_1    conda-forge
q2-alignment              2020.2.0                 py36_0    qiime2/label/r2020.2
q2-composition            2020.2.0                 py36_0    qiime2/label/r2020.2
q2-cutadapt               2020.2.0                 py36_0    qiime2/label/r2020.2
q2-dada2                  2020.2.0                 py36_0    qiime2/label/r2020.2
q2-deblur                 2020.2.0                 py36_0    qiime2/label/r2020.2
q2-demux                  2020.2.0                 py36_0    qiime2/label/r2020.2
q2-diversity              2020.2.0                 py36_0    qiime2/label/r2020.2
q2-emperor                2020.2.0                 py36_0    qiime2/label/r2020.2
q2-feature-classifier     2020.2.0                 py36_0    qiime2/label/r2020.2
q2-feature-table          2020.2.0                 py36_0    qiime2/label/r2020.2
q2-fragment-insertion     2020.2.0                 py36_0    qiime2/label/r2020.2
q2-gneiss                 2020.2.0                 py36_0    qiime2/label/r2020.2
q2-longitudinal           2020.2.0                 py36_0    qiime2/label/r2020.2
q2-metadata               2020.2.0                 py36_0    qiime2/label/r2020.2
q2-phylogeny              2020.2.0                 py36_0    qiime2/label/r2020.2
q2-quality-control        2020.2.0                 py36_0    qiime2/label/r2020.2
q2-quality-filter         2020.2.0                 py36_0    qiime2/label/r2020.2
q2-sample-classifier      2020.2.0                 py36_0    qiime2/label/r2020.2
q2-taxa                   2020.2.0                 py36_0    qiime2/label/r2020.2
q2-types                  2020.2.0                 py36_0    qiime2/label/r2020.2
q2-vsearch                2020.2.0                 py36_0    qiime2/label/r2020.2
q2cli                     2020.2.0                 py36_0    qiime2/label/r2020.2
q2templates               2020.2.0                 py36_0    qiime2/label/r2020.2
qiime2                    2020.2.0                 py36_0    qiime2/label/r2020.2
qt                        5.9.7                h52cfd70_2    conda-forge
r-assertthat              0.2.1             r35h6115d3f_1    conda-forge
r-backports               1.1.5             r35hcdcec82_0    conda-forge
r-base                    3.5.1             h08e1455_1008    conda-forge
r-bh                      1.72.0_3          r35h6115d3f_0    conda-forge
r-bitops                  1.0_6           r35hcdcec82_1003    conda-forge
r-cli                     2.0.2             r35h6115d3f_0    conda-forge
r-cluster                 2.1.0             r35h9bbef5b_2    conda-forge
r-colorspace              1.4_1             r35hcdcec82_1    conda-forge
r-crayon                  1.3.4            r351h6115d3f_1    conda-forge
r-data.table              1.12.6            r35hcdcec82_0    conda-forge
r-digest                  0.6.25            r35h0357c0b_1    conda-forge
r-ellipsis                0.3.0             r35hcdcec82_0    conda-forge
r-fansi                   0.4.1             r35hcdcec82_0    conda-forge
r-farver                  2.0.3             r35h0357c0b_0    conda-forge
r-formatr                 1.7               r35h6115d3f_1    conda-forge
r-futile.logger           1.4.3            r351h6115d3f_1    conda-forge
r-futile.options          1.0.1            r351h6115d3f_0    conda-forge
r-ggplot2                 3.2.1             r35h6115d3f_0    conda-forge
r-glue                    1.3.1             r35hcdcec82_1    conda-forge
r-gtable                  0.3.0             r35h6115d3f_2    conda-forge
r-hwriter                 1.3.2            r351h6115d3f_1    conda-forge
r-labeling                0.3              r351h6115d3f_1    conda-forge
r-lambda.r                1.2.4             r35h6115d3f_0    conda-forge
r-lattice                 0.20_40           r35hcdcec82_0    conda-forge
r-latticeextra            0.6_28           r351h6115d3f_1    conda-forge
r-lazyeval                0.2.2             r35hcdcec82_1    conda-forge
r-lifecycle               0.1.0             r35h6115d3f_0    conda-forge
r-magrittr                1.5              r351h6115d3f_1    conda-forge
r-mass                    7.3_51.5          r35hcdcec82_0    conda-forge
r-matrix                  1.2_18            r35h7fa42b6_2    conda-forge
r-matrixstats             0.55.0            r35hcdcec82_0    conda-forge
r-mgcv                    1.8_31            r35hcdcec82_0    conda-forge
r-munsell                 0.5.0            r351h6115d3f_1    conda-forge
r-nlme                    3.1_144           r35h9bbef5b_0    conda-forge
r-permute                 0.9_5             r35h6115d3f_2    conda-forge
r-pillar                  1.4.3             r35h6115d3f_0    conda-forge
r-pkgconfig               2.0.3             r35h6115d3f_0    conda-forge
r-plyr                    1.8.5             r35h0357c0b_0    conda-forge
r-r6                      2.4.1             r35h6115d3f_0    conda-forge
r-rcolorbrewer            1.1_2            r351h6115d3f_1    conda-forge
r-rcpp                    1.0.3             r35h0357c0b_0    conda-forge
r-rcppparallel            4.4.4             r35h0357c0b_0    conda-forge
r-rcurl                   1.98_1.1          r35hcdcec82_0    conda-forge
r-reshape2                1.4.3           r35h0357c0b_1004    conda-forge
r-rlang                   0.4.4             r35hcdcec82_0    conda-forge
r-scales                  1.1.0             r35h6115d3f_0    conda-forge
r-snow                    0.4_3            r351h6115d3f_0    conda-forge
r-stringi                 1.4.3             r35h0357c0b_2    conda-forge
r-stringr                 1.4.0             r35h6115d3f_1    conda-forge
r-tibble                  2.1.3             r35hcdcec82_1    conda-forge
r-utf8                    1.1.4           r35hcdcec82_1002    conda-forge
r-vctrs                   0.2.3             r35hcdcec82_0    conda-forge
r-vegan                   2.5_6             r35hbf399a0_1    conda-forge
r-viridislite             0.3.0            r351h6115d3f_1    conda-forge
r-withr                   2.1.2            r351h6115d3f_0    conda-forge
r-zeallot                 0.1.0           r35h6115d3f_1001    conda-forge
raxml                     8.2.12               h516909a_2    bioconda
readline                  8.0                  h46ee950_1    conda-forge
requests                  2.23.0           py36h9f0ad1d_1    conda-forge
scikit-bio                0.5.5           py36h3010b51_1000    conda-forge
scikit-learn              0.22.1           py36hcdab131_1    conda-forge
scipy                     1.4.1            py36h2d22cac_3    conda-forge
seaborn                   0.10.0                     py_1    conda-forge
send2trash                1.5.0                      py_0    conda-forge
sepp                      4.3.10           py36heb1dbbb_2    bioconda
setuptools                45.2.0                   py36_0    conda-forge
sina                      1.6.0                hc7f9b0f_0    bioconda
sip                       4.19.8          py36hf484d3e_1000    conda-forge
six                       1.14.0                   py36_0    conda-forge
sortmerna                 2.0                  he860b03_4    bioconda
sqlite                    3.30.1               hcee41ef_0    conda-forge
statsmodels               0.11.1           py36h8c4c3a4_2    conda-forge
tbb                       2019.9               hc9558a2_1    conda-forge
terminado                 0.8.3            py36h9f0ad1d_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tk                        8.6.10               hed695b0_1    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
tornado                   6.0.3            py36h516909a_4    conda-forge
traitlets                 4.3.3            py36h9f0ad1d_1    conda-forge
tzlocal                   2.0.0                      py_0    conda-forge
unifrac                   0.10.0           py36h6bb024c_1    bioconda
urllib3                   1.25.7           py36h9f0ad1d_1    conda-forge
vsearch                   2.7.0                         1    bioconda
wcwidth                   0.1.8              pyh9f0ad1d_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.34.2                   py36_0    conda-forge
widgetsnbextension        3.5.1            py36h9f0ad1d_4    conda-forge
xopen                     0.8.4            py36h9f0ad1d_1    conda-forge
xorg-fixesproto           5.0               h14c3975_1002    conda-forge
xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.10               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxtst              1.2.3             h516909a_1002    conda-forge
xorg-recordproto          1.14.2            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h516909a_1002    conda-forge
yaml                      0.2.2                h516909a_1    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zipp                      3.0.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.4.4                h3b9ef0a_2    conda-forge

[nick-youngblut]

I am running barnap on 100's of genomes, and this error is only occurring for a few of them, which makes it seem to be input-specific, but the genome files appear to be valid.

Is the error caused by a lack of usable output by nhmmer?

[greboul]

It's been more than a year since Nick reported this issue and I recently encountered it too.

After hours of wondering i finally looked into the tool perl code and found why; it's simply because of line 99 in the executable (in bin dir): err("nhmmer failed to run - $_") if m/fail|error|core dump|bus error/i;

In Nick's first caption, the file path contained the fail word - X361_fail_Common_Opossum__maxbin2__High.001.fna
And that perl line looks for that and therefore thinks that it is a fail error message from nhmmer...

So changing just the directories or the files name that barrnap is using to avoid any of those key words used in line 99 regex in the path is going to fix the error. Definitely something that can be improved easily if a Barrnap.10 is coming

[jvollme]

@greboul: Thanks, that helped me figure out my problem too! In my case this error occurs whenever the infput fasta files contain the substring "error" somewhere in the filename.
Weird bug but luckily fixable if one knows the problem...