Describe the bug
When I run funannotate compare, I enter the annotation results of 2 species for comparison, and it can run successfully, but when I enter the annotation results of 3 species, an error occurs.
What command did you issue?
funannotate-docker compare -i GLeI1521_XWZ.gbk GLeI1615_BMK.gbk --cpus 80
funannotate-docker compare -i GLeI1521_BMK.gbk GLeI1521_XWZ.gbk GLeI1615_BMK.gbk --cpus 80
Logfiles
$cat compare2.pbs.e168371
logname: no login name
logname: no login name
[May 16 10:00 AM]: OS: Debian GNU/Linux 10, 80 cores, ~ 1584 GB RAM. Python: 3.8.12
[May 16 10:00 AM]: Running 1.8.17
[May 16 10:00 AM]: Now parsing 2 genomes
[May 16 10:00 AM]: working on Ganoderma leucocontextum
[May 16 10:01 AM]: working on Ganoderma leucocontextum
[May 16 10:01 AM]: No secondary metabolite annotations found
[May 16 10:01 AM]: Summarizing PFAM domain results
Fontconfig error: No writable cache directories
[May 16 10:01 AM]: Summarizing InterProScan results
[May 16 10:01 AM]: Loading InterPro descriptions
[May 16 10:01 AM]: Summarizing MEROPS protease results
[May 16 10:01 AM]: found 12/87 MEROPS familes with stdev >= 1.000000
[May 16 10:01 AM]: Summarizing CAZyme results
[May 16 10:01 AM]: found 11/105 CAZy familes with stdev >= 1.000000
[May 16 10:01 AM]: Summarizing COG results
[May 16 10:01 AM]: Summarizing secreted protein results
[May 16 10:01 AM]: Summarizing fungal transcription factors
[May 16 10:01 AM]: Running GO enrichment for each genome
[May 16 11:47 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...
[May 16 11:48 AM]: Compiling all annotations for each genome
[May 16 11:48 AM]: Skipping RAxML phylogeny as at least 4 taxa are required
[May 16 11:48 AM]: Compressing results to output file: funannotate_compare.tar.gz
[May 16 11:49 AM]: Funannotate compare completed successfully!
$cat compare1.pbs.e168370
logname: no login name
logname: no login name
[May 16 09:00 AM]: OS: Debian GNU/Linux 10, 80 cores, ~ 1584 GB RAM. Python: 3.8.12
[May 16 09:00 AM]: Running 1.8.17
[May 16 09:00 AM]: Now parsing 3 genomes
[May 16 09:00 AM]: working on Ganoderma leucocontextum
[May 16 09:00 AM]: working on Ganoderma leucocontextum
[May 16 09:01 AM]: working on Ganoderma leucocontextum
[May 16 09:01 AM]: No secondary metabolite annotations found
[May 16 09:01 AM]: Summarizing PFAM domain results
Fontconfig error: No writable cache directories
[May 16 09:01 AM]: Summarizing InterProScan results
[May 16 09:01 AM]: Loading InterPro descriptions
[May 16 09:01 AM]: Summarizing MEROPS protease results
[May 16 09:01 AM]: found 14/87 MEROPS familes with stdev >= 1.000000
[May 16 09:01 AM]: Summarizing CAZyme results
[May 16 09:01 AM]: found 16/105 CAZy familes with stdev >= 1.000000
[May 16 09:01 AM]: Summarizing COG results
[May 16 09:01 AM]: Summarizing secreted protein results
[May 16 09:01 AM]: Summarizing fungal transcription factors
[May 16 09:01 AM]: Running GO enrichment for each genome
[May 16 10:35 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...
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 717, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/compare.py", line 1254, in main
if row != "*":
File "/venv/lib/python3.8/site-packages/pandas/core/generic.py", line 1466, in nonzero
raise ValueError(
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
OS/Install Information
output of funannotate check --show-versions
$funannotate-docker check --show-versions
Checking dependencies for 1.8.17
You are running Python v 3.8.12. Now checking python packages...
biopython: 1.79
goatools: 1.3.11
matplotlib: 3.7.3
natsort: 8.4.0
numpy: 1.22.4
pandas: 2.0.3
psutil: 5.9.8
requests: 2.31.0
scikit-learn: 0.24.2
scipy: 1.5.3
seaborn: 0.13.0
All 11 python packages installed
Are you using the latest release? yes V1.8.17
Describe the bug When I run funannotate compare, I enter the annotation results of 2 species for comparison, and it can run successfully, but when I enter the annotation results of 3 species, an error occurs.
What command did you issue? funannotate-docker compare -i GLeI1521_XWZ.gbk GLeI1615_BMK.gbk --cpus 80 funannotate-docker compare -i GLeI1521_BMK.gbk GLeI1521_XWZ.gbk GLeI1615_BMK.gbk --cpus 80
Logfiles $cat compare2.pbs.e168371 logname: no login name logname: no login name [May 16 10:00 AM]: OS: Debian GNU/Linux 10, 80 cores, ~ 1584 GB RAM. Python: 3.8.12 [May 16 10:00 AM]: Running 1.8.17 [May 16 10:00 AM]: Now parsing 2 genomes [May 16 10:00 AM]: working on Ganoderma leucocontextum [May 16 10:01 AM]: working on Ganoderma leucocontextum [May 16 10:01 AM]: No secondary metabolite annotations found [May 16 10:01 AM]: Summarizing PFAM domain results Fontconfig error: No writable cache directories [May 16 10:01 AM]: Summarizing InterProScan results [May 16 10:01 AM]: Loading InterPro descriptions [May 16 10:01 AM]: Summarizing MEROPS protease results [May 16 10:01 AM]: found 12/87 MEROPS familes with stdev >= 1.000000 [May 16 10:01 AM]: Summarizing CAZyme results [May 16 10:01 AM]: found 11/105 CAZy familes with stdev >= 1.000000 [May 16 10:01 AM]: Summarizing COG results [May 16 10:01 AM]: Summarizing secreted protein results [May 16 10:01 AM]: Summarizing fungal transcription factors [May 16 10:01 AM]: Running GO enrichment for each genome [May 16 11:47 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile... [May 16 11:48 AM]: Compiling all annotations for each genome [May 16 11:48 AM]: Skipping RAxML phylogeny as at least 4 taxa are required [May 16 11:48 AM]: Compressing results to output file: funannotate_compare.tar.gz [May 16 11:49 AM]: Funannotate compare completed successfully!
$cat compare1.pbs.e168370 logname: no login name logname: no login name [May 16 09:00 AM]: OS: Debian GNU/Linux 10, 80 cores, ~ 1584 GB RAM. Python: 3.8.12 [May 16 09:00 AM]: Running 1.8.17 [May 16 09:00 AM]: Now parsing 3 genomes [May 16 09:00 AM]: working on Ganoderma leucocontextum [May 16 09:00 AM]: working on Ganoderma leucocontextum [May 16 09:01 AM]: working on Ganoderma leucocontextum [May 16 09:01 AM]: No secondary metabolite annotations found [May 16 09:01 AM]: Summarizing PFAM domain results Fontconfig error: No writable cache directories [May 16 09:01 AM]: Summarizing InterProScan results [May 16 09:01 AM]: Loading InterPro descriptions [May 16 09:01 AM]: Summarizing MEROPS protease results [May 16 09:01 AM]: found 14/87 MEROPS familes with stdev >= 1.000000 [May 16 09:01 AM]: Summarizing CAZyme results [May 16 09:01 AM]: found 16/105 CAZy familes with stdev >= 1.000000 [May 16 09:01 AM]: Summarizing COG results [May 16 09:01 AM]: Summarizing secreted protein results [May 16 09:01 AM]: Summarizing fungal transcription factors [May 16 09:01 AM]: Running GO enrichment for each genome [May 16 10:35 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile... Traceback (most recent call last): File "/venv/bin/funannotate", line 8, in
sys.exit(main())
File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 717, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/compare.py", line 1254, in main
if row != "*":
File "/venv/lib/python3.8/site-packages/pandas/core/generic.py", line 1466, in nonzero
raise ValueError(
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
OS/Install Information
output of
funannotate check --show-versions$funannotate-docker check --show-versionsChecking dependencies for 1.8.17
You are running Python v 3.8.12. Now checking python packages... biopython: 1.79 goatools: 1.3.11 matplotlib: 3.7.3 natsort: 8.4.0 numpy: 1.22.4 pandas: 2.0.3 psutil: 5.9.8 requests: 2.31.0 scikit-learn: 0.24.2 scipy: 1.5.3 seaborn: 0.13.0 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: 1.855 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 threads: 2.15 threads::shared: 1.56 ERROR: local::lib not installed, install with cpanm local::lib
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=/usr/share/augustus/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: 3.3.2 bamtools: bamtools 2.5.2 bedtools: bedtools v2.31.1 blat: BLAT v35 diamond: 2.1.8 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2017-11-15 hisat2: 2.2.1 hmmscan: HMMER 3.4 (Aug 2023) hmmsearch: HMMER 3.4 (Aug 2023) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.26-r1175 pigz: 2.8 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 49 tbl2asn: 25.8 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