Not sure if this is a bug or just an install issue. Using version 1.8.9 within Singularity and getting an error on plotting the summary charts. Doesn't seem to be finding bioperl installed as dependency, maybe that is issue?
[Mar 19 11:33 AM]: Summarizing MEROPS protease results
[Mar 19 11:33 AM]: found 14/100 MEROPS familes with stdev >= 1.000000
Error received:
Traceback (most recent call last):
File "/venv/bin/funannotate", line 8, in
sys.exit(main())
File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 711, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/compare.py", line 540, in main
lib.drawHeatmap(meropsplot, 'BuPu', os.path.join(
File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 7893, in drawHeatmap
cbar_ax = fig.add_axes(shrink=0.4)
File "/venv/lib/python3.8/site-packages/matplotlib/figure.py", line 619, in add_axes
raise TypeError(
TypeError: add_axes() missing 1 required positional argument: 'rect'
Logfiles
see above
OS/Install Information
output of funannotate check --show-versions
$ singularity run --cleanenv funannotate.sif funannotate check --show-versions
Checking dependencies for 1.8.10
You are running Python v 3.8.12. Now checking python packages...
biopython: 1.77
goatools: 1.2.3
matplotlib: 3.5.1
natsort: 8.1.0
numpy: 1.22.3
pandas: 1.4.2
psutil: 5.9.0
requests: 2.27.1
scikit-learn: 1.0.2
scipy: 1.5.3
seaborn: 0.11.2
All 11 python packages installed
Not sure if this is a bug or just an install issue. Using version 1.8.9 within Singularity and getting an error on plotting the summary charts. Doesn't seem to be finding bioperl installed as dependency, maybe that is issue?
Copy/paste the command used.
Running funcompare with singularity
singularity run --bind $PWD --pwd $PWD funannotate.sif funannotate compare -i /genome1/funannotate/ /genome2/funannotate/ /genome3/funannotate/ -o /local/storage/usr/showa28/fun_compare_beaugenus_only/ --cpus 32
Most everything ran OK through this step:
[Mar 19 11:33 AM]: Summarizing MEROPS protease results [Mar 19 11:33 AM]: found 14/100 MEROPS familes with stdev >= 1.000000
Error received:
Traceback (most recent call last): File "/venv/bin/funannotate", line 8, in
sys.exit(main())
File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 711, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/compare.py", line 540, in main
lib.drawHeatmap(meropsplot, 'BuPu', os.path.join(
File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 7893, in drawHeatmap
cbar_ax = fig.add_axes(shrink=0.4)
File "/venv/lib/python3.8/site-packages/matplotlib/figure.py", line 619, in add_axes
raise TypeError(
TypeError: add_axes() missing 1 required positional argument: 'rect'
Logfiles see above
OS/Install Information
funannotate check --show-versions$ singularity run --cleanenv funannotate.sif funannotate check --show-versions
Checking dependencies for 1.8.10
You are running Python v 3.8.12. Now checking python packages... biopython: 1.77 goatools: 1.2.3 matplotlib: 3.5.1 natsort: 8.1.0 numpy: 1.22.3 pandas: 1.4.2 psutil: 5.9.0 requests: 2.27.1 scikit-learn: 1.0.2 scipy: 1.5.3 seaborn: 0.11.2 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: 1.855 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: 2.000024 threads: 2.15 threads::shared: 1.56 ERROR: Bio::Perl not installed, install with cpanm Bio::Perl
Checking Environmental Variables... $FUNANNOTATE_DB=/opt/databases $PASAHOME=/venv/opt/pasa-2.4.1 $TRINITYHOME=/venv/opt/trinity-2.8.5 $EVM_HOME=/venv/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/venv/config ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v36 diamond: 2.0.15 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.9.1-internal kallisto: 0.46.1 mafft: v7.505 (2022/Apr/10) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: pigz 2.6 proteinortho: 6.0.16 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.12 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 31 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: gmes_petap.pl not installed ERROR: signalp not installed