prokka
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20 hours ago •
tseemann
tseemann
Prokka runing error: Could not run command: cat, parallel, blastp
There is a prokka software running error has been bothering me for many days.
First, the error content and log file prompt is: [17:29:43] Could not run command: cat test3.prokka/test.sprot.tmp.45976.faa | parallel --gnu --plain -j 8 --block 15534 --recstart '>' --pipe blastp -query - -db /Userdata/data_lwc/software/prokka-master/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > test3.prokka/test.sprot.tmp.45976.blast 2> /dev/null
Second, at first I suspected it was the prokka version or the source. I used Prokka's 1.11; Versions 1.12 and 1.14 of the software. Version 1.14 is from Conda, and the other two are downloaded packages.
All three versions have the same error, so I think it is due to the software dependency problem.
Then, I updated the Parallel software and BLAST + software mentioned in the error report. Parallel uses the latest version, and I tried 2.8.1 of Blast + software. 2.9.0; 2.10.1; 2.11.0 and 2.12.0. But the problem has not gone away.
In the end, I ran the command separately, and no error was reported. In addition, I tried the server of another node with shared storage and the Conda installed version 1.14 of Prokka worked fine.
So, I assume it's not the software, the same files can run on other servers. I guess it's still the software, but I can't find any clues.
Hi @liweicheng0011!
Have you tried the Bioconda version of Prokka (https://bioconda.github.io/recipes/prokka/README.html)? Just curious if that might work better for you
I have the same issue with Prokka v1.14.6 installed using conda on our HPC. A local installation works however.
[13:51:16] Could not run command: cat IN01_pass\/IN01\.proteins\.tmp\.23937\.faa | parallel --gnu --plain -j 4 --block 177369 --recstart '>' --pipe blastp -query - -db IN01_pass/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > IN01_pass\/IN01\.proteins\.tmp\.23937\.blast 2> /dev/null
# packages in environment at /rds/general/user/ywan/home/anaconda3/envs/prokka1.14:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
aragorn 1.2.38 h779adbc_4 bioconda
atk-1.0 2.36.0 h3371d22_4 conda-forge
barrnap 0.9 hdfd78af_4 bioconda
bedtools 2.30.0 h7d7f7ad_1 bioconda
blast 2.11.0 pl526he19e7b1_0 bioconda
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h7f98852_1 conda-forge
ca-certificates 2021.5.30 ha878542_0 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2021.5.30 py37h89c1867_0 conda-forge
clustalw 2.1 h7d875b9_6 bioconda
curl 7.77.0 hea6ffbf_0 conda-forge
entrez-direct 13.9 pl5262he881be0_2 bioconda
expat 2.4.1 h9c3ff4c_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.1 hba837de_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.6 h04a7f16_0 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.47.2 h85b4f2f_0 conda-forge
gtk2 2.24.33 h539f30e_1 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
harfbuzz 2.8.1 h83ec7ef_0 conda-forge
hmmer 3.3.2 h1b792b2_1 bioconda
icu 68.1 h58526e2_0 conda-forge
infernal 1.1.4 h779adbc_0 bioconda
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
krb5 1.19.1 hcc1bbae_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge
lerc 2.2.1 h9c3ff4c_0 conda-forge
libcurl 7.77.0 h2574ce0_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 9.3.0 h2828fa1_19 conda-forge
libgd 2.3.2 h78a0170_0 conda-forge
libglib 2.68.3 h3e27bee_0 conda-forge
libgomp 9.3.0 h2828fa1_19 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn11 1.34 h1cef754_0 conda-forge
libnghttp2 1.43.0 h812cca2_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
librsvg 2.50.7 hc3c00ef_0 conda-forge
libssh2 1.9.0 ha56f1ee_6 conda-forge
libstdcxx-ng 9.3.0 h6de172a_19 conda-forge
libtiff 4.3.0 hf544144_1 conda-forge
libtool 2.4.6 h58526e2_1007 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.0 h3452ae3_0 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.13 h7f98852_1003 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libxslt 1.1.33 h15afd5d_2 conda-forge
lz4-c 1.9.3 h9c3ff4c_0 conda-forge
minced 0.4.2 hdfd78af_1 bioconda
ncurses 6.2 h58526e2_4 conda-forge
openjdk 11.0.9.1 h5cc2fde_1 conda-forge
openssl 1.1.1k h7f98852_0 conda-forge
paml 4.9 h779adbc_6 bioconda
pango 1.48.5 hb8ff022_0 conda-forge
parallel 20210422 ha770c72_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-aceperl 1.92 pl526_2 bioconda
perl-algorithm-diff 1.1903 pl526_2 bioconda
perl-algorithm-munkres 0.08 pl526_1 bioconda
perl-apache-test 1.40 pl526_1 bioconda
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-appconfig 1.71 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-array-compare 3.0.1 pl526_1 bioconda
perl-autoloader 5.74 pl526_2 bioconda
perl-base 2.23 pl526_1 bioconda
perl-bio-asn1-entrezgene 1.73 pl5262hdfd78af_2 bioconda
perl-bio-coordinate 1.007001 pl5262hdfd78af_2 bioconda
perl-bio-featureio 1.6.905 pl5262hdfd78af_3 bioconda
perl-bio-phylo 0.58 pl5262hdfd78af_3 bioconda
perl-bio-samtools 1.43 pl526h1341992_1 bioconda
perl-bio-tools-phylo-paml 1.7.3 pl5262hdfd78af_2 bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4 pl5262hdfd78af_2 bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4 pl5262hdfd78af_3 bioconda
perl-bioperl 1.7.2 pl526_11 bioconda
perl-bioperl-core 1.007002 pl5262hdfd78af_3 bioconda
perl-bioperl-run 1.007002 pl5262hdfd78af_5 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-cache-cache 1.08 pl526_0 bioconda
perl-capture-tiny 0.48 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-cgi 4.44 pl526h14c3975_1 bioconda
perl-class-data-inheritable 0.08 pl526_1 bioconda
perl-class-inspector 1.34 pl526_0 bioconda
perl-class-load 0.25 pl526_0 bioconda
perl-class-load-xs 0.10 pl526h6bb024c_2 bioconda
perl-class-method-modifiers 2.12 pl526_0 bioconda
perl-clone 0.42 pl526h516909a_0 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-convert-binary-c 0.78 pl526h6bb024c_3 bioconda
perl-convert-binhex 1.125 pl526_1 bioconda
perl-crypt-rc4 2.02 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-data-optlist 0.110 pl526_2 bioconda
perl-data-stag 0.14 pl526_1 bioconda
perl-date-format 2.30 pl526_2 bioconda
perl-db-file 1.855 pl526h516909a_0 bioconda
perl-dbd-sqlite 1.64 pl526h516909a_0 bioconda
perl-dbi 1.642 pl526_0 bioconda
perl-devel-globaldestruction 0.14 pl526_0 bioconda
perl-devel-overloadinfo 0.005 pl526_0 bioconda
perl-devel-stacktrace 2.04 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-digest-perl-md5 1.9 pl526_1 bioconda
perl-digest-sha1 2.13 pl526h6bb024c_1 bioconda
perl-dist-checkconflicts 0.11 pl526_2 bioconda
perl-dynaloader 1.25 pl526_1 bioconda
perl-email-date-format 1.005 pl526_2 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-error 0.17027 pl526_1 bioconda
perl-eval-closure 0.14 pl526h6bb024c_4 bioconda
perl-exception-class 1.44 pl526_0 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-slurp-tiny 0.004 pl526_1 bioconda
perl-file-sort 1.01 pl526_2 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-file-which 1.23 pl526_0 bioconda
perl-font-afm 1.20 pl526_2 bioconda
perl-font-ttf 1.06 pl526_0 bioconda
perl-gd 2.68 pl526he941832_0 bioconda
perl-getopt-long 2.50 pl526_1 bioconda
perl-graph 0.9704 pl526_1 bioconda
perl-graphviz 2.24 pl526h734ff71_0 bioconda
perl-html-element-extended 1.18 pl526_1 bioconda
perl-html-entities-numbered 0.04 pl526_1 bioconda
perl-html-formatter 2.16 pl526_0 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tableextract 2.13 pl526_2 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tidy 1.60 pl526_0 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-html-treebuilder-xpath 0.14 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-image-info 1.38 pl526_1 bioconda
perl-image-size 3.300 pl526_2 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-sessiondata 1.03 pl526_1 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-string 1.08 pl526_3 bioconda
perl-io-stringy 2.111 pl526_1 bioconda
perl-io-tty 1.12 pl526_1 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-ipc-run 20180523.0 pl526_0 bioconda
perl-ipc-sharelite 0.17 pl526h6bb024c_1 bioconda
perl-jcode 2.07 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-lib 0.63 pl526_1 bioconda
perl-libwww-perl 6.39 pl526_0 bioconda
perl-libxml-perl 0.08 pl526_2 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-lwp-simple 6.15 pl526h470a237_4 bioconda
perl-mailtools 2.21 pl526_0 bioconda
perl-math-cdf 0.1 pl526h14c3975_5 bioconda
perl-math-derivative 1.01 pl526_0 bioconda
perl-math-random 0.72 pl526h14c3975_2 bioconda
perl-math-spline 0.02 pl526_2 bioconda
perl-mime-base64 3.15 pl526_1 bioconda
perl-mime-lite 3.030 pl526_1 bioconda
perl-mime-tools 5.508 pl526_1 bioconda
perl-mime-types 2.17 pl526_0 bioconda
perl-mldbm 2.05 pl526_1 bioconda
perl-module-implementation 0.09 pl526_2 bioconda
perl-module-runtime 0.016 pl526_1 bioconda
perl-module-runtime-conflicts 0.003 pl526_0 bioconda
perl-moo 2.003004 pl526_0 bioconda
perl-moose 2.2011 pl526hf484d3e_1 bioconda
perl-mozilla-ca 20180117 pl526_1 bioconda
perl-mro-compat 0.13 pl526_0 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-ole-storage_lite 0.19 pl526_3 bioconda
perl-package-deprecationmanager 0.17 pl526_0 bioconda
perl-package-stash 0.38 pl526hf484d3e_1 bioconda
perl-package-stash-xs 0.28 pl526hf484d3e_1 bioconda
perl-params-util 1.07 pl526h6bb024c_4 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-parse-recdescent 1.967015 pl526_0 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-pdf-api2 2.035 pl526_0 bioconda
perl-pod-escapes 1.07 pl526_1 bioconda
perl-pod-usage 1.69 pl526_1 bioconda
perl-postscript 0.06 pl526_2 bioconda
perl-role-tiny 2.000008 pl526_0 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-set-scalar 1.29 pl526_2 bioconda
perl-soap-lite 1.19 pl526_1 bioconda
perl-socket 2.027 pl526_1 bioconda
perl-sort-naturally 1.03 pl526_2 bioconda
perl-spreadsheet-parseexcel 0.65 pl526_2 bioconda
perl-spreadsheet-writeexcel 2.40 pl526_2 bioconda
perl-statistics-descriptive 3.0702 pl526_0 bioconda
perl-storable 3.15 pl526h14c3975_0 bioconda
perl-sub-exporter 0.987 pl526_2 bioconda
perl-sub-exporter-progressive 0.001013 pl526_0 bioconda
perl-sub-identify 0.14 pl526h14c3975_0 bioconda
perl-sub-install 0.928 pl526_2 bioconda
perl-sub-name 0.21 pl526_1 bioconda
perl-sub-quote 2.006003 pl526_1 bioconda
perl-sub-uplevel 0.2800 pl526h14c3975_2 bioconda
perl-svg 2.84 pl526_0 bioconda
perl-svg-graph 0.02 pl526_3 bioconda
perl-task-weaken 1.06 pl526_0 bioconda
perl-template-toolkit 2.26 pl526_1 bioconda
perl-test 1.26 pl526_1 bioconda
perl-test-deep 1.128 pl526_1 bioconda
perl-test-differences 0.67 pl526_0 bioconda
perl-test-exception 0.43 pl526_2 bioconda
perl-test-harness 3.42 pl526_0 bioconda
perl-test-leaktrace 0.16 pl526h14c3975_2 bioconda
perl-test-most 0.35 pl526_0 bioconda
perl-test-requiresinternet 0.05 pl526_0 bioconda
perl-test-warn 0.36 pl526_1 bioconda
perl-text-diff 1.45 pl526_0 bioconda
perl-tie-ixhash 1.23 pl526_2 bioconda
perl-time-hires 1.9760 pl526h14c3975_1 bioconda
perl-time-local 1.28 pl526_1 bioconda
perl-timedate 2.30 pl526_1 bioconda
perl-tree-dag_node 1.31 pl526_0 bioconda
perl-try-tiny 0.30 pl526_1 bioconda
perl-type-tiny 1.004004 pl526_0 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-unicode-map 0.112 pl526h6bb024c_3 bioconda
perl-uri 1.76 pl526_0 bioconda
perl-www-robotrules 6.02 pl526_3 bioconda
perl-xml-dom 1.46 pl526_0 bioconda
perl-xml-dom-xpath 0.14 pl526_1 bioconda
perl-xml-filter-buffertext 1.01 pl526_2 bioconda
perl-xml-libxml 2.0132 pl526h7ec2d77_1 bioconda
perl-xml-libxslt 1.94 pl526_1 bioconda
perl-xml-namespacesupport 1.12 pl526_0 bioconda
perl-xml-parser 2.44_01 pl5262hc3e0081_1002 conda-forge
perl-xml-regexp 0.04 pl526_2 bioconda
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-sax-writer 0.57 pl526_0 bioconda
perl-xml-simple 2.25 pl526_1 bioconda
perl-xml-twig 3.52 pl526_2 bioconda
perl-xml-writer 0.625 pl526_2 bioconda
perl-xml-xpath 1.44 pl526_0 bioconda
perl-xml-xpathengine 0.14 pl526_2 bioconda
perl-xsloader 0.24 pl526_0 bioconda
perl-yaml 1.29 pl526_0 bioconda
pip 21.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
prodigal 2.6.3 h779adbc_3 bioconda
prokka 1.14.6 pl5262hdfd78af_1 bioconda
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
python 3.7.10 hffdb5ce_100_cpython conda-forge
python_abi 3.7 1_cp37m conda-forge
readline 8.1 h46c0cb4_0 conda-forge
setuptools 49.6.0 py37h89c1867_3 conda-forge
sqlite 3.35.5 h74cdb3f_0 conda-forge
t_coffee 11.0.8 py37hea885bf_8 bioconda
tbl2asn-forever 25.7.2f h779adbc_1 bioconda
tidyp 1.04 h779adbc_3 bioconda
tk 8.6.10 h21135ba_1 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.5.0 ha95c52a_0 conda-forge
I have the same issue with Prokka v1.14.6.
Running: cat PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.faa | parallel --gnu --plain -j 4 --block 2321 --recstart '>' --pipe blastp -query - -db /home/huyujie/miniconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.blast 2> /dev/null
Could not run command: cat PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.faa | parallel --gnu --plain -j 4 --block 2321 --recstart '>' --pipe blastp -query - -db /home/huyujie/miniconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.blast 2> /dev/null
