barrnap
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Published
20 hours ago •
tseemann
tseemann
[barrnap] ERROR: nhmmer failed to run
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
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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
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raxml 8.2.12 h516909a_2 bioconda
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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
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six 1.14.0 py36_0 conda-forge
sortmerna 2.0 he860b03_4 bioconda
sqlite 3.30.1 hcee41ef_0 conda-forge
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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?
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
@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...
