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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Prokka runing error: Could not run command: cat, parallel, blastp #586

Open liweicheng0011 opened 3 years ago

liweicheng0011 commented 3 years ago

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.

rpetit3 commented 3 years ago

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

liweicheng0011 commented 3 years ago

I tried Version 1.14 is from Conda, but there had same error.

wanyuac commented 3 years ago

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
yujiehu0823 commented 3 years ago

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

sam-mic commented 3 years ago

Please refer to #402 sevance's answer. It works.