Closed cdixo closed 1 year ago
nextgenusfs
commented
2 years ago Seems like your environment is not quite right, I've never seen an error like you are getting when the script runs. But I guess following the error, did you try to pass --PASAHOME /opt/conda/opt/pasa-2.4.1
cdixo
commented
2 years ago Hi @nextgenusfs, thanks for the super quick reply. Turns out, I just made one of those simple coding errors that fouled up the whole thing.
I am running a container with all of the components necessary to run funannotate within it. To actually run my scripts as a job on my university's supercomputer, I first submit a submission through sbatch in which I run the submission script which later calls my script I actually want to run. First, I have to turn on my container within the submission script /fs/project/PAS1444/software/funannotate/funannotate_mask.sif and then, in actual script I want to run, my first line needs to load in the source file source /fs/project/PAS1444/software/funannotate/source.sh . Unfortunately, I forgot to include the call to turn on the source code in the script.
Sorry for taking up your time but hopefully this will jog someone else's memory in the future to check for this and maybe help them resolve their coding error too.
I was waiting to see if everything would run smoothly before closing the thread, but It seems to be running smoothly so far so I will close this thread.
Thanks again for the help,
Cullen
Are you using the latest release? Yes - 1.8.14
Describe the bug Trying to run funannotate update command with new transcriptomic data to update a pre-existing .gff genome annotation file. When doing so, error is given of "AttributeError: module 'funannotate.library' has no attribute 'log' ". When providing an output destination to the command, it changes the error to "$PASAHOME environmental variable not found, PASA is not properly configured. You can use the --PASAHOME argument to specifiy a path at runtime"
Thank you for your help in advance!
What command did you issue? 1st try:
2nd try:
Logfiles 1st try log file:
2nd try log file:
OS/Install Information
funannotate check --show-versionsChecking dependencies for 1.8.14
You are running Python v 3.7.6. Now checking python packages... biopython: 1.78 goatools: 1.0.6 matplotlib: 3.2.1 natsort: 7.0.1 numpy: 1.19.1 pandas: 1.1.2 psutil: 5.7.2 requests: 2.22.0 scikit-learn: 0.23.2 scipy: 1.5.2 seaborn: 0.11.0 All 11 python packages installed
You are running Perl v b'5.026002'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.852 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.29 local::lib: 2.000029 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/fs/project/PAS1444/databases/funannotate/ $PASAHOME=/opt/conda/opt/pasa-2.4.1 $TRINITY_HOME=/opt/conda/opt/trinity-2.8.5 $EVM_HOME=/opt/conda/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/fs/project/PAS1444/databases/augustus/config/ $GENEMARK_PATH=/fs/project/PAS1444/software/gmes_linux_64_4/ All 6 environmental variables are set
Checking external dependencies... Traceback (most recent call last): File "/opt/conda/bin/ete3", line 6, in
from ete3.tools.ete import main
File "/opt/conda/lib/python3.7/site-packages/ete3/tools/ete.py", line 55, in
from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view,
File "/opt/conda/lib/python3.7/site-packages/ete3/tools/ete_view.py", line 48, in
from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace,
ImportError: cannot import name 'TextFace' from 'ete3' (/opt/conda/lib/python3.7/site-packages/ete3/init.py)
PASA: 2.4.1
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.3.3
bamtools: bamtools 2.5.1
bedtools: bedtools v2.29.2
blat: BLAT v36
diamond: 2.0.4
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2017-11-15
hisat2: 2.2.1
hmmscan: HMMER 3.3.1 (Jul 2020)
hmmsearch: HMMER 3.3.1 (Jul 2020)
java: 11.0.8-internal
kallisto: 0.46.1
mafft: v7.471 (2020/Jul/3)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.17-r941
proteinortho: 6.0.22
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.7
snap: 2006-07-28
stringtie: 2.1.2
tRNAscan-SE: 2.0.6 (May 2020)
tantan: tantan 13
tbl2asn: no way to determine, likely 25.X
tblastn: tblastn 2.2.31+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
ERROR: emapper.py not installed
ERROR: ete3 not installed
ERROR: gmes_petap.pl not installed
ERROR: pigz not installed
ERROR: signalp not installed
conda listpackages in environment at /opt/conda:
Name Version Build Channel
_libgcc_mutex 0.1 main _r-mutex 1.0.1 anacondar_1 conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge asn1crypto 1.3.0 py37_0 augustus 3.3.3 pl526hce533f5_0 bioconda bamtools 2.5.1 he513fc3_6 bioconda bedtools 2.29.2 hc088bd4_0 bioconda binutils_impl_linux-64 2.33.1 he1b5a44_7 conda-forge binutils_linux-64 2.33.1 h9595d00_17 conda-forge biopython 1.78 py37h8f50634_0 conda-forge blast 2.2.31 pl526h3066fca_3 bioconda blat 36 0 bioconda boost 1.70.0 py37h9de70de_1 conda-forge boost-cpp 1.70.0 ha2d47e9_1 conda-forge bowtie 1.3.0 py37h9a982cc_1 bioconda bowtie2 2.4.1 py37h8270d21_3 bioconda bwidget 1.9.14 0 conda-forge bzip2 1.0.8 h516909a_3 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge cairo 1.16.0 h18b612c_1001 conda-forge cdbtools 0.99 he513fc3_5 bioconda certifi 2020.6.20 py37hc8dfbb8_0 conda-forge cffi 1.14.0 py37h2e261b9_0 chardet 3.0.4 py37_1003 clustalw 2.1 hc9558a2_5 bioconda codingquarry 2.0 py37h9a982cc_4 bioconda conda 4.8.5 py37hc8dfbb8_1 conda-forge conda-package-handling 1.6.0 py37h7b6447c_0 cryptography 2.8 py37h1ba5d50_0 curl 7.68.0 hf8cf82a_0 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 he372182_0 conda-forge diamond 2.0.4 h56fc30b_0 bioconda distro 1.5.0 pyh9f0ad1d_0 conda-forge entrez-direct 13.9 pl526h375a9b1_0 bioconda ete3 3.1.2 pyh9f0ad1d_0 conda-forge evidencemodeler 1.1.1 2 bioconda exonerate 2.4.0 haf93ef1_3 bioconda expat 2.2.9 he1b5a44_2 conda-forge fasta3 36.3.8 h516909a_5 bioconda fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.10.2 he06d7ca_0 conda-forge funannotate 1.8.1 pyh3252c3a_0 bioconda gcc_impl_linux-64 7.3.0 habb00fd_1 gcc_linux-64 7.3.0 h553295d_17 conda-forge gettext 0.19.8.1 hc5be6a0_1002 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 2.66.0 h0dae87d_0 conda-forge glimmerhmm 3.0.4 pl526hf484d3e_3 bioconda gmap 2017.11.15 h2f06484_4 bioconda goatools 1.0.6 pyh864c0ab_1 bioconda graphite2 1.3.13 he1b5a44_1001 conda-forge graphviz 2.38.0 hf68f40c_1011 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_1 gxx_linux-64 7.3.0 h553295d_17 conda-forge h5py 2.10.0 nompi_py37h513d04c_102 conda-forge harfbuzz 2.4.0 h37c48d4_1 conda-forge hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge hisat2 2.2.1 he1b5a44_2 bioconda hmmer 3.3.1 he1b5a44_0 bioconda htslib 1.9 h4da6232_3 bioconda icu 58.2 hf484d3e_1000 conda-forge idna 2.8 py37_0 infernal 1.1.2 h516909a_3 bioconda iqtree 2.0.3 h176a8bc_0 bioconda joblib 0.16.0 py_0 conda-forge jpeg 9d h516909a_0 conda-forge k8 0.2.5 he513fc3_0 bioconda kallisto 0.46.1 h4f7b962_0 bioconda kiwisolver 1.2.0 py37h99015e2_0 conda-forge kmer-jellyfish 2.3.0 hc9558a2_1 bioconda krb5 1.16.4 h173b8e3_0 lcms2 2.11 hbd6801e_0 conda-forge ld_impl_linux-64 2.33.1 h53a641e_7 libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libcurl 7.68.0 hda55be3_0 conda-forge libdb 6.1.26 0 bioconda libdeflate 1.2 h516909a_1 bioconda libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgd 2.2.5 h0d07dcb_1005 conda-forge libgfortran-ng 7.5.0 hdf63c60_16 conda-forge libiconv 1.16 h516909a_0 conda-forge libidn11 1.34 h1cef754_0 conda-forge liblapack 3.8.0 11_openblas conda-forge liblapacke 3.8.0 11_openblas conda-forge libopenblas 0.3.6 h6e990d7_6 conda-forge libpng 1.6.37 hed695b0_2 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.1.0 hc3755c2_3 conda-forge libtool 2.4.6 h516909a_1005 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libwebp 1.0.2 h56121f0_5 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.9 h13577e0_2 conda-forge libxslt 1.1.32 hae48121_1003 conda-forge lighttpd 1.4.53 h76df0ec_0 conda-forge llvm-meta 7.0.0 0 conda-forge lp_solve 5.5.2.5 h14c3975_1001 conda-forge lxml 4.4.1 py37h7ec2d77_0 conda-forge lz4-c 1.8.3 he1b5a44_1001 conda-forge mafft 7.471 h516909a_0 bioconda matplotlib-base 3.2.1 py37hef1b27d_0 metis 5.1.0 he1b5a44_1006 conda-forge minimap2 2.17 hed695b0_3 bioconda mysql-connector-c 6.1.6 2 bioconda natsort 7.0.1 py_0 conda-forge ncurses 6.2 he6710b0_0 numpy 1.19.1 py37h7ea13bd_2 conda-forge openblas 0.3.6 h6e990d7_6 conda-forge openjdk 11.0.8 hacce0ff_0 conda-forge openmp 7.0.0 h2d50403_0 conda-forge openssl 1.1.1h h516909a_0 conda-forge paml 4.9 h516909a_5 bioconda pandas 1.1.2 py37h3340039_0 conda-forge pango 1.40.14 he7ab937_1005 conda-forge pasa 2.4.1 he1b5a44_0 bioconda patsy 0.5.1 py_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h516909a_1006 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 pl526_1 bioconda perl-bio-coordinate 1.007001 pl526_1 bioconda perl-bio-featureio 1.6.905 pl526_2 bioconda perl-bio-phylo 0.58 pl526_2 bioconda perl-bio-samtools 1.43 pl526h1341992_1 bioconda perl-bio-tools-phylo-paml 1.7.3 pl526_1 bioconda perl-bio-tools-run-alignment-clustalw 1.7.4 pl526_1 bioconda perl-bio-tools-run-alignment-tcoffee 1.7.4 pl526_2 bioconda perl-bioperl 1.7.2 pl526_11 bioconda perl-bioperl-core 1.007002 pl526_2 bioconda perl-bioperl-run 1.007002 pl526_4 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-clone-choose 0.010 pl526_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-cpan-meta 2.150010 pl526_0 bioconda perl-cpan-meta-requirements 2.140 pl526_0 bioconda perl-cpan-meta-yaml 0.018 pl526_0 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 1.852 pl526h14c3975_0 bioconda perl-dbd-mysql 4.046 pl526h2d50403_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-cbuilder 0.280230 pl526_1 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-extutils-manifest 1.72 pl526_0 bioconda perl-extutils-parsexs 3.35 pl526_0 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 2.71 pl526he860b03_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-hash-merge 0.300 pl526_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-cmd 1.02 pl526_0 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-pp 4.04 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-locale-maketext-simple 0.21 pl526_2 bioconda perl-logger-simple 2.0 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-build 0.4224 pl526_3 bioconda perl-module-corelist 5.20190524 pl526_0 bioconda perl-module-implementation 0.09 pl526_2 bioconda perl-module-load 0.32 pl526_1 bioconda perl-module-load-conditional 0.68 pl526_2 bioconda perl-module-metadata 1.000036 pl526_0 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-object-insideout 4.05 pl526_0 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-parallel-forkmanager 2.02 pl526_0 bioconda perl-params-check 0.38 pl526_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-perl-ostype 1.010 pl526_1 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-scalar-util-numeric 0.40 pl526_1 bioconda 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bioconda perl-test-leaktrace 0.16 pl526h14c3975_2 bioconda perl-test-most 0.35 pl526_0 bioconda perl-test-pod 1.52 pl526_0 bioconda perl-test-requiresinternet 0.05 pl526_0 bioconda perl-test-warn 0.36 pl526_1 bioconda perl-text-abbrev 1.02 pl526_0 bioconda perl-text-diff 1.45 pl526_0 bioconda perl-text-parsewords 3.30 pl526_0 bioconda perl-text-soundex 3.05 pl526_1000 conda-forge 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-version 0.9924 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 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