funannotate
funannotate copied to clipboard
nextgenusfs
test failure
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp
Checking duplication of 6 contigs
-----------------------------------------------
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153
scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858
scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
-----------------------------------------------
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file
[Jan 07 06:03 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 07 06:03 PM]: Running funanotate v1.8.8
[Jan 07 06:03 PM]: Soft-masking simple repeats with tantan
[Jan 07 06:03 PM]: Repeat soft-masking finished:
Masked genome: /home/xly/test-mask_3e5d9525-c3bd-4e21-a33a-26163f920c78/test.masked.fa
num scaffolds: 2
assembly size: 1,216,048 bp
masked repeats: 50,965 bp (4.19%)
-------------------------------------------------------
-------------------------------------------------------
-------------------------------------------------------
[Jan 07 06:03 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 07 06:03 PM]: Running funannotate v1.8.8
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in <module>
sys.exit(main())
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 472, in main
for f in os.listdir(os.path.join(LOCALAUGUSTUS, 'species', aug_species)):
FileNotFoundError: [Errno 2] No such file or directory: 'annotate/predict_misc/ab_initio_parameters/augustus/species/saccharomyces'
#########################################################
Running `funannotate clean` unit testing: minimap2 mediated assembly duplications
CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive
#########################################################
#########################################################
SUCCESS: `funannotate clean` test complete.
#########################################################
#########################################################
Running `funannotate mask` unit testing: RepeatModeler --> RepeatMasker
CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 40
#########################################################
#########################################################
SUCCESS: `funannotate mask` test complete.
#########################################################
#########################################################
Running `funannotate predict` unit testing
CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 40 --species Awesome testicus
#########################################################
#########################################################
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in <module>
sys.exit(main())
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 405, in main
runPredictTest(args)
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 160, in runPredictTest
assert 1500 <= countGFFgenes(os.path.join(
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 45, in countGFFgenes
with open(input, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'test-predict_3e5d9525-c3bd-4e21-a33a-26163f920c78/annotate/predict_results/Awesome_testicus.gff3'
-----------------------------------------------
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp
Checking duplication of 6 contigs
-----------------------------------------------
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153
scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858
scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
-----------------------------------------------
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file
[Jan 07 06:03 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 07 06:03 PM]: Running funanotate v1.8.8
[Jan 07 06:03 PM]: Soft-masking simple repeats with tantan
[Jan 07 06:03 PM]: Repeat soft-masking finished:
Masked genome: /home/xly/test-mask_5892f6a6-65ca-452d-9ecb-3621e7db9c94/test.masked.fa
num scaffolds: 2
assembly size: 1,216,048 bp
masked repeats: 50,965 bp (4.19%)
-------------------------------------------------------
-------------------------------------------------------
-------------------------------------------------------
[Jan 07 06:03 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 07 06:03 PM]: Running funannotate v1.8.8
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in <module>
sys.exit(main())
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 472, in main
for f in os.listdir(os.path.join(LOCALAUGUSTUS, 'species', aug_species)):
FileNotFoundError: [Errno 2] No such file or directory: 'annotate/predict_misc/ab_initio_parameters/augustus/species/saccharomyces'
#########################################################
Running `funannotate clean` unit testing: minimap2 mediated assembly duplications
CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive
#########################################################
#########################################################
SUCCESS: `funannotate clean` test complete.
#########################################################
#########################################################
Running `funannotate mask` unit testing: RepeatModeler --> RepeatMasker
CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 40
#########################################################
#########################################################
SUCCESS: `funannotate mask` test complete.
#########################################################
#########################################################
Running `funannotate predict` unit testing
CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 40 --species Awesome testicus
#########################################################
#########################################################
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in <module>
sys.exit(main())
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 405, in main
runPredictTest(args)
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 160, in runPredictTest
assert 1500 <= countGFFgenes(os.path.join(
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 45, in countGFFgenes
with open(input, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'test-predict_5892f6a6-65ca-452d-9ecb-3621e7db9c94/annotate/predict_results/Awesome_testicus.gff3'
-------------------------------------------------------
Checking dependencies for 1.8.8
-------------------------------------------------------
To print all dependencies and versions: funannotate check --show-versions
You are running Python v 3.8.15. Now checking python packages...
All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules...
All 27 Perl modules installed
Checking Environmental Variables...
All 6 environmental variables are set
-------------------------------------------------------
Checking external dependencies...
All 36 external dependencies are installed
(funannotate) xly@wyb-PowerEdge-R920:~$ funannotate check --show-versions
-------------------------------------------------------
Checking dependencies for 1.8.8
-------------------------------------------------------
You are running Python v 3.8.15. Now checking python packages...
biopython: 1.80
goatools: 1.2.3
matplotlib: 3.4.3
natsort: 8.2.0
numpy: 1.24.1
pandas: 1.5.2
psutil: 5.9.4
requests: 2.28.1
scikit-learn: 1.2.0
scipy: 1.10.0
seaborn: 0.12.2
All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules...
Bio::Perl: 1.7.4
Carp: 1.50
Clone: 0.46
DBD::SQLite: 1.72
DBD::mysql: 4.050
DBI: 1.643
DB_File: 1.855
Data::Dumper: 2.183
File::Basename: 2.85
File::Which: 1.24
Getopt::Long: 2.54
Hash::Merge: 0.302
JSON: 4.10
LWP::UserAgent: 6.67
Logger::Simple: 2.0
POSIX: 1.94
Parallel::ForkManager: 2.02
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.14
Tie::File: 1.06
URI::Escape: 5.12
YAML: 1.30
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed
Checking Environmental Variables...
$FUNANNOTATE_DB=/home/xly/soft/mambaforge-pypy3/envs/funannotate/funannotate_db
$PASAHOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/pasa-2.5.2
$TRINITY_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/trinity-2.8.5
$EVM_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/config
$GENEMARK_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin
All 6 environmental variables are set
-------------------------------------------------------
Checking external dependencies...
PASA: 2.5.2
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.5.0
bamtools: bamtools 2.5.1
bedtools: bedtools v2.30.0
blat: BLAT v35
diamond: 2.0.15
emapper.py: 2.1.9
ete3: 3.1.2
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2021-08-25
gmes_petap.pl: 4.71_lic
hisat2: 2.2.1
hmmscan: HMMER 3.3.2 (Nov 2020)
hmmsearch: HMMER 3.3.2 (Nov 2020)
java: 17.0.3-internal
kallisto: 0.46.1
mafft: v7.508 (2022/Sep/07)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.24-r1122
proteinortho: 6.1.7
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.16.1
signalp: 5.0b
snap: 2006-07-28
stringtie: 2.2.1
tRNAscan-SE: 2.0.11 (Oct 2022)
tantan: tantan 40
tbl2asn: no way to determine, likely 25.X
tblastn: tblastn 2.2.31+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
All 36 external dependencies are installed
I don't know why stop,and i hope you can reply! thanky very much!
Augustus v3.5 is not compatible with the version of funannotate you are running, downgrade Augustus.
after i downgrade Augustus,still failure
(funannotate) xly@wyb-PowerEdge-R920:~$ funannotate test -t all --cpus 40
#########################################################
Running funannotate clean unit testing: minimap2 mediated assembly duplications
Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive
#########################################################
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp Checking duplication of 6 contigs
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153 scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858 scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file
#########################################################
SUCCESS: funannotate clean test complete.
#########################################################
#########################################################
Running funannotate mask unit testing: RepeatModeler --> RepeatMasker
Downloading: https://osf.io/hbryz/download?version=1 Bytes: 375687 CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 40
#########################################################
[Jan 08 01:26 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15 [Jan 08 01:26 PM]: Running funanotate v1.8.8 [Jan 08 01:26 PM]: Soft-masking simple repeats with tantan [Jan 08 01:26 PM]: Repeat soft-masking finished: Masked genome: /home/xly/test-mask_1d0df229-9e70-473a-8ae4-4c0124cd388f/test.masked.fa num scaffolds: 2 assembly size: 1,216,048 bp masked repeats: 50,965 bp (4.19%)
#########################################################
SUCCESS: funannotate mask test complete.
#########################################################
#########################################################
Running funannotate predict unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 40 --species Awesome testicus]]]]]]]]]]]]#########################################################
[Jan 08 01:26 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 08 01:26 PM]: Running funannotate v1.8.8
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in
(funannotate) xly@wyb-PowerEdge-R920:~$ funannotate check --show-versions
Checking dependencies for 1.8.8
You are running Python v 3.8.15. Now checking python packages... biopython: 1.80 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.2.0 numpy: 1.24.1 pandas: 1.5.2 psutil: 5.9.4 requests: 2.28.1 scikit-learn: 1.2.0 scipy: 1.10.0 seaborn: 0.12.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Bio::Perl: 1.7.4 Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/home/xly/soft/mambaforge-pypy3/envs/funannotate/funannotate_db $PASAHOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/config/ $GENEMARK_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin All 6 environmental variables are set
Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.4.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.71_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 proteinortho: 6.1.7 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 All 36 external dependencies are installed
after i downgrade Augustus,still failure (funannotate) @.***:~$ funannotate test -t all --cpus 40 ######################################################### Running funannotate clean unit testing: minimap2 mediated assembly duplications Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive #########################################################
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp Checking duplication of 6 contigs
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153 scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858 scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file ######################################################### SUCCESS: funannotate clean test complete. #########################################################
######################################################### Running funannotate mask unit testing: RepeatModeler --> RepeatMasker Downloading: https://osf.io/hbryz/download?version=1 Bytes: 375687 CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 40 #########################################################
[Jan 08 01:26 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15 [Jan 08 01:26 PM]: Running funanotate v1.8.8 [Jan 08 01:26 PM]: Soft-masking simple repeats with tantan [Jan 08 01:26 PM]: Repeat soft-masking finished: Masked genome: /home/xly/test-mask_1d0df229-9e70-473a-8ae4-4c0124cd388f/test.masked.fa num scaffolds: 2 assembly size: 1,216,048 bp masked repeats: 50,965 bp (4.19%)
######################################################### SUCCESS: funannotate mask test complete. #########################################################
######################################################### Running funannotate predict unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 40 --species Awesome testicus]]]]]]]]]]]]#########################################################
[Jan 08 01:26 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15 [Jan 08 01:26 PM]: Running funannotate v1.8.8 Traceback (most recent call last): File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in sys.exit(main()) File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 472, in main for f in os.listdir(os.path.join(LOCALAUGUSTUS, 'species', aug_species)): FileNotFoundError: [Errno 2] No such file or directory: 'annotate/predict_misc/ab_initio_parameters/augustus/species/saccharomyces' ######################################################### Traceback (most recent call last): File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in sys.exit(main()) File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 405, in main runPredictTest(args) File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 160, in runPredictTest assert 1500 <= countGFFgenes(os.path.join( File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 45, in countGFFgenes with open(input, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'test-predict_1d0df229-9e70-473a-8ae4-4c0124cd388f/annotate/predict_results/Awesome_testicus.gff3'
(funannotate) @.***:~$ funannotate check --show-versions
Checking dependencies for 1.8.8
You are running Python v 3.8.15. Now checking python packages... biopython: 1.80 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.2.0 numpy: 1.24.1 pandas: 1.5.2 psutil: 5.9.4 requests: 2.28.1 scikit-learn: 1.2.0 scipy: 1.10.0 seaborn: 0.12.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Bio::Perl: 1.7.4 Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/home/xly/soft/mambaforge-pypy3/envs/funannotate/funannotate_db $PASAHOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/config/ $GENEMARK_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin All 6 environmental variables are set
Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.4.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.71_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 proteinortho: 6.1.7 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 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 All 36 external dependencies are installed
------------------ 原始邮件 ------------------ 发件人: "Jon @.>; 发送时间: 2023年1月8日(星期天) 中午12:32 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [nextgenusfs/funannotate] test failure (Issue #852)
Augustus v3.5 is not compatible with the version of funannotate you are running, downgrade Augustus.
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
You have an old version of funannotate, try upgrading to latest in master with pip.
now i install the funannotate V1.8.14 and augutus V 3.4.0 but still not work and i check export AUGUSTUS_CONFIG_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/config we can see species exist (funannotate) xly 11:20:05 ~/soft/mambaforge-pypy3/envs/funannotate/config/species $ ll total 584 drwxr-xr-x 144 xly students 12288 1月 8 13:23 ./ drwxr-xr-x 7 xly students 4096 1月 8 13:23 ../ drwxr-xr-x 2 xly students 4096 1月 8 13:23 adorsata/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 aedes/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 amphimedon/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 ancylostoma_ceylanicum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 anidulans/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 arabidopsis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Argopecten_irradians/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 aspergillus_fumigatus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 aspergillus_nidulans/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 aspergillus_oryzae/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 aspergillus_terreus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Aurelia_aurita/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Bathycoccus_prasinos/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 bombus_impatiens1/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 bombus_terrestris2/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 botrytis_cinerea/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 b_pseudomallei/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 brugia/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 cacao/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 caenorhabditis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 camponotus_floridanus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 candida_albicans/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 candida_guilliermondii/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 candida_tropicalis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Cassiopea_xamachana/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 c_elegans_trsk/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 chaetomium_globosum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 chicken/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 chiloscyllium/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 chlamy2011/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 chlamydomonas/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Chlamydomonas_eustigma/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 chlorella/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Chloropicon_primus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Chrysaora_chesapeakeij/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 ciona/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 coccidioides_immitis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Conidiobolus_coronatus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 coprinus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 coprinus_cinereus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 coyote_tobacco/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 cryptococcus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 cryptococcus_neoformans_gattii/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 cryptococcus_neoformans_neoformans_B/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 cryptococcus_neoformans_neoformans_JEC21/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 culex/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 debaryomyces_hansenii/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Dunaliella_salina/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 E_coli_K12/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Ectocarpus_siliculosus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 elephant_shark/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Encephalitozoon_cuniculi/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 encephalitozoon_cuniculi_GB/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 eremothecium_gossypii/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Fistulifera_solaris/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 fly/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 fly_exp/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Fragilariopsis_cylindrus_CCMP1102/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 fusarium/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 fusarium_graminearum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 galdieria/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 generic/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 gigaspora_margarita/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Gonapodya_prolifera/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 heliconius_melpomene1/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 histoplasma/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 histoplasma_capsulatum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 honeybee1/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 human/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 hymenolepis_microstoma/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 japaneselamprey/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 kluyveromyces_lactis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 laccaria_bicolor/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 leishmania_tarentolae/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 lodderomyces_elongisporus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 magnaporthe_grisea/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 maize/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 maize5/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Micromonas_commoda/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Micromonas_pusilla/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 mnemiopsis_leidyi/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Monoraphidium_neglectum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 nasonia/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 nematostella_vectensis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Nemopilema_nomurai/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 neurospora/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 neurospora_crassa/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Notospermus_geniculatus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Ostreococcus_sp_lucimarinus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Ostreococcus_tauri/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 parasteatoda/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 pchrysosporium/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 pea_aphid/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 pfalciparum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Phaeodactylum_tricornutum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 phanerochaete_chrysosporium/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 pichia_stipitis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 pisaster/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 pneumocystis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Pseudo-nitzschia_multistriata/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Ptychodera_flava/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Raphidocelis_subcapitata/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 rhincodon/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 rhizopus_oryzae/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 rhodnius/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Rhopilema_esculentum/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 rice/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 saccharomyces/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 saccharomyces_cerevisiae_rm11-1a_1/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 saccharomyces_cerevisiae_S288C/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 s_aureus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 schistosoma/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 schistosoma2/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 schizosaccharomyces_pombe/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 scyliorhinus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 sealamprey/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Sordaria_macrospora/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Sphaceloma_murrayae/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 s_pneumoniae/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 strongylocentrotus_purpuratus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 sulfolobus_solfataricus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 sunflower/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 template_prokaryotic/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 tetrahymena/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Thalassiosira_pseudonana_CCMP1335/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 thermoanaerobacter_tengcongensis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 tomato/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 toxoplasma/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 tribolium2012/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 trichinella/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Trichoplax_adhaerens/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 ustilago/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 ustilago_maydis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 verticillium_albo_atrum1/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 verticillium_longisporum1/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Vitrella_brassicaformis/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 volvox/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 wheat/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Xiphophorus_maculatus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 Xipophorus_maculatus/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 yarrowia_lipolytica/ drwxr-xr-x 2 xly students 4096 1月 8 13:23 zebrafish/ so i try to install Augustus=3.3.0 but Could not solve for environment specs Encountered problems while solving:
- package augustus-3.3-boost1.64_1 requires boost 1.64*, but none of the providers can be installed
funannotate check --show-versions
Checking dependencies for 1.8.14
You are running Python v 3.8.15. Now checking python packages... biopython: 1.80 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.2.0 numpy: 1.24.1 pandas: 1.5.2 psutil: 5.9.4 requests: 2.28.1 scikit-learn: 1.2.0 scipy: 1.10.0 seaborn: 0.12.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/home/xly/soft/mambaforge-pypy3/envs/funannotate/funannotate_db $PASAHOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/xly/soft/mambaforge-pypy3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/config/ $GENEMARK_PATH=/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin All 6 environmental variables are set
Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.4.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.71_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.1.7 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 All 37 external dependencies are installed
(funannotate) xly 11:11:47 ~
$
cd work/test/
(funannotate) xly 11:12:03 ~/work/test
$
ll
total 8
drwxr-xr-x 2 xly students 4096 1月 9 11:04 ./
drwxr-xr-x 3 xly students 4096 1月 7 15:55 ../
(funannotate) xly 11:12:04 ~/work/test
$
funannotate test -t all --cpus 40
#########################################################
Running funannotate clean unit testing: minimap2 mediated assembly duplications
Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive
#########################################################
minimap2 version=2.24-r1122 path=/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/minimap2
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp Checking duplication of 6 contigs
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153 scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858 scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file
#########################################################
SUCCESS: funannotate clean test complete.
#########################################################
#########################################################
Running funannotate mask unit testing: RepeatModeler --> RepeatMasker
Downloading: https://osf.io/hbryz/download?version=1 Bytes: 375687 CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 40
#########################################################
[Jan 09 11:12 AM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15 [Jan 09 11:12 AM]: Running funanotate v1.8.14 [Jan 09 11:12 AM]: Soft-masking simple repeats with tantan [Jan 09 11:12 AM]: Repeat soft-masking finished: Masked genome: /home/xly/work/test/test-mask_4bdea6eb-1df2-41a3-a9db-a4c6efe97985/test.masked.fa num scaffolds: 2 assembly size: 1,216,048 bp masked repeats: 50,965 bp (4.19%)
#########################################################
SUCCESS: funannotate mask test complete.
#########################################################
#########################################################
Running funannotate predict unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 40 --species Awesome testicus]]]]]]]]]]]]#########################################################
[Jan 09 11:12 AM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 09 11:12 AM]: Running funannotate v1.8.14
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in
it seems still not predict successful，do you know why its happening? hope to your reply thank you very much!
still not work
(funannotate) xly 16:29:48 ~/work/test
$
funannotate test -t all --cpus 40
#########################################################
Running funannotate clean unit testing: minimap2 mediated assembly duplications
Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive
#########################################################
minimap2 version=2.24-r1122 path=/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/minimap2
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp Checking duplication of 6 contigs
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153 scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858 scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file
#########################################################
SUCCESS: funannotate clean test complete.
#########################################################
#########################################################
Running funannotate mask unit testing: RepeatModeler --> RepeatMasker
Downloading: https://osf.io/hbryz/download?version=1 Bytes: 375687 CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 40
#########################################################
[Jan 09 04:30 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15 [Jan 09 04:30 PM]: Running funanotate v1.8.14 [Jan 09 04:30 PM]: Soft-masking simple repeats with tantan [Jan 09 04:30 PM]: Repeat soft-masking finished: Masked genome: /home/xly/work/test/test-mask_b067f083-87a9-4ae3-939c-025aaddc1fdc/test.masked.fa num scaffolds: 2 assembly size: 1,216,048 bp masked repeats: 50,965 bp (4.19%)
#########################################################
SUCCESS: funannotate mask test complete.
#########################################################
#########################################################
Running funannotate predict unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 40 --species Awesome testicus]]]]]]]]]]]]#########################################################
[Jan 09 04:30 PM]: OS: Ubuntu 22.04, 120 cores, ~ 1057 GB RAM. Python: 3.8.15
[Jan 09 04:30 PM]: Running funannotate v1.8.14
Traceback (most recent call last):
File "/home/xly/soft/mambaforge-pypy3/envs/funannotate/bin/funannotate", line 8, in
Funannotate Databases currently installed:
Database Type Version Date Num_Records Md5checksum merops diamond 12.0 2017-10-04 5009 a6dd76907896708f3ca5335f58560356 uniprot diamond 2022_05 2022-12-14 568744 4a1e2f62101e6a1334b0fd4e07590b86 dbCAN hmmer3 10.0 2021-10-03 641 04696dfba1c3bb82ff9b72cfbb3e4a65 pfam hmmer3 35.0 2021-11 19632 c78ab387de299860bd242d6f57930c7f repeats diamond 1.0 2022-06-27 11950 4e8cafc3eea47ec7ba505bb1e3465d21 go text 2023-01-01 2023-01-01 47417 f2a0667c060b688fa4c4afa59f7a783a mibig diamond 1.4 2022-06-27 31023 118f2c11edde36c81bdea030a0228492 interpro xml 92.0 2022-12-07 38349 2480c914dc697b2943c3f891836e81af busco_outgroups outgroups 1.0 2023-01-09 8 6795b1d4545850a4226829c7ae8ef058 gene2product text 1.85 2022-12-21 34346 8e9890350a07045a7c0e291bb0f78af3
To update a database type: funannotate setup -i DBNAME -d /home/xly/soft/mambaforge-pypy3/envs/funannotate/funannotate_db --force
To see install BUSCO outgroups type: funannotate database --show-outgroups
To see BUSCO tree type: funannotate database --show-buscos
can you check in what is in annotate/predict_misc/ab_initio_parameters
something maybe did not download fully? can you just run funannotate test -t predict ?
for f in os.listdir(os.path.join(LOCALAUGUSTUS, 'species', aug_species)):
FileNotFoundError: [Errno 2] No such file or directory: 'annotate/predict_misc/ab_initio_parameters/augustus/species/saccharomyces'
Hi all, I run software installs on a HPC and install funannotate using conda. In order to allow multiple users to run the software, I wrote a script that copies the augustus config dir into a user-writeable space.
Therefore, each user will have a copy of the config dir and will be able to write into that dir. Then, the script writes the shell commands to their screen and puts a copy in their home dir so they can source that file and have their augustus config dir set for them.
So that's the setup for my comments.
I had a user write in that they were having an issue with funannotate and had the same error message as above. I replicated the issue on my end.
I then ran a raw augustus --proteinprofile --species saccharomyes command to see what the error message was, and it was a config dir not found error. My script did not set up the $AUGUSTUS_CONFIG_PATH properly, and the directory was not found.
However, the error message from funannotate does not indicate what the actual augustus error was.
Here's my question, is there a way to turn on the logging of augustus errors, or forward those errors outside of funannotate presently? If not, can you capture the STDERR from the subprocess call and forward it to us so we can see the issue? I can probably dig through the code and find it to turn it on, but my time is tight at the moment.
Is it possible that there is some other augustus config and/or setting that is causing this error? I don't think this particular user is having the same problem we were, but if others come looking for help when using a centrally-installed funannotate, it may be difficult for people to figure out why there is an augustus error message.
Thoughts?
Same issue. How to reproduce:
module load conda
conda clean -y -a
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --set channel_priority flexible
conda config --set solver libmamba
conda create -y -n funannotate-1.8.13 -c predector -c bioconda funannotate=1.8.13 'python>=3.6,<3.9' 'augustus<3.4' perl-local-lib perl-dbd-mysql eggnog-mapper pigz signalp5
funannotate setup -d /scratch/mirror/funannotate/funannotate_db
ln -s /scratch/mirror/eggnog-mapper/2.1.9/ /home/apps/conda/miniconda3/envs/funannotate-1.8.13/lib/python3.8/site-packages/data
conda activate funannotate-1.8.13
# module load genemarkes
export FUNANNOTATE_DB=/scratch/mirror/funannotate/funannotate_db
export AUGUSTUS_CONFIG_PATH=$HOME/augustus/config
funannotate check --show-versions˙
funannotate --test -t predict
Output from last command:
-------------------------------------------------------
[Feb 17 02:16 PM]: OS: Oracle Linux Server 8.7, 128 cores, ~ 528 GB RAM. Python: 3.8.15
[Feb 17 02:16 PM]: Running funannotate v1.8.13
[Feb 17 02:16 PM]: Skipping CodingQuarry as no --rna_bam passed
[Feb 17 02:16 PM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus pretrained
genemark selftraining
glimmerhmm busco
snap busco
augustus: ERROR
PP::Profile: Error parsing pattern file"/home/apps/conda/miniconda3/envs/funannotate-1.8.13/lib/python3.8/site-packages/funannotate/config/EOG092C0B3U.prfl", line 8.
[Feb 17 02:16 PM]: ERROR: augustus --proteinprofile test failed, likely a compilation error. This is required to run BUSCO, exiting.
Output from log file:
$cat test-predict_794a477b-8fd0-4dac-82f6-b9529cef0b4e/annotate/logfiles/funannotate-predict.log
[02/17/23 13:52:55]: /home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 2 --species Awesome testicus
[02/17/23 13:52:55]: OS: Oracle Linux Server 8.7, 128 cores, ~ 528 GB RAM. Python: 3.8.15
[02/17/23 13:52:55]: Running funannotate v1.8.13
[02/17/23 13:52:55]: GeneMark path: /home/apps/genemarkes/4.71
[02/17/23 13:52:55]: Full path to gmes_petap.pl: /home/apps/genemarkes/4.71/gmes_petap.pl
[02/17/23 13:52:55]: GeneMark appears to be functional? True
[02/17/23 13:52:55]: exonerate version=exonerate 2.4.0 path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/exonerate
[02/17/23 13:52:55]: diamond version=2.0.15 path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/diamond
[02/17/23 13:52:55]: tbl2asn version=no way to determine, likely 25.X path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/tbl2asn
[02/17/23 13:52:55]: bedtools version=bedtools v2.30.0 path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/bedtools
[02/17/23 13:52:55]: augustus version=3.3.3 path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/augustus
[02/17/23 13:52:55]: etraining version=NA path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/etraining
[02/17/23 13:52:55]: tRNAscan-SE version=2.0.11 (Oct 2022) path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/tRNAscan-SE
[02/17/23 13:52:55]: bam2hints version=NA path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/bam2hints
[02/17/23 13:52:55]: minimap2 version=2.24-r1122 path=/home/apps/conda/miniconda3/envs/funannotate-1.8.13/bin/minimap2
[02/17/23 13:52:55]: $AUGUSTUS_CONFIG_PATH=/scratch/students/apptest/fun/config
[02/17/23 13:52:56]: {'augustus': 1, 'hiq': 2, 'genemark': 1, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1}
[02/17/23 13:52:56]: Skipping CodingQuarry as no --rna_bam passed
[02/17/23 13:52:56]: {'augustus': 'pretrained', 'genemark': 'selftraining', 'snap': 'busco', 'glimmerhmm': 'busco'}
[02/17/23 13:52:56]: Parsed training data, run ab-initio gene predictors as follows:
[02/17/23 13:52:56]: ERROR: augustus --proteinprofile test failed, likely a compilation error. This is required to run BUSCO, exiting.
I've tried augustus 3.3, 3.4 and 3.5 as mentioned in #862. I also tried upgrading funannotate with:
conda activate funannotate-1.8.13
python -m pip install git+https://github.com/nextgenusfs/funannotate.git --upgrade --force --no-deps
Without success...
Are you getting same Augustus complication error with Augustus 3.5 and funannotate latest (v1.8.14)? If so, I'd try manual compilation of Augustus (I'm not familiar with oracle Linux to know if that is an issue). Augustus is finicky.
Thanks for the quick reply. Indeed same error with augustus 3.5 and funannotate 1.8.14. ˙Augustus seems to work otherwise. Would you happen to know what the augustus command is that fails? I'll try self-compiled augustus though, just to be sure.
The check functionality python code is here: https://github.com/nextgenusfs/funannotate/blob/master/funannotate/library.py#L1005
What this is running to check if Augustus ppx (protein profile mode) is working is this:
augustus --proteinprofile=/path/to/your/python/lib/site-packages/funannotate/config/EOG092C0B3U.prfl \
--species=anidulans /path/to/your/python/lib/site-packages/funannotate/config/busco_test.fa
If Augustus is functional you'll get a prediction, if there is a compilation error it will output the error you are seeing in the log file.
You can grab the two files and run this outside of funannotate as well: https://raw.githubusercontent.com/nextgenusfs/funannotate/master/funannotate/config/EOG092C0B3U.prfl https://raw.githubusercontent.com/nextgenusfs/funannotate/master/funannotate/config/busco_test.fa
I found my error!!! Thanks for the support! @nextgenusfs
When I copied the augustus config dir, the parameters dir wasn't transferred. This resolved it:
rm -r config
# cp -r $(conda info --base)/envs/funannotate-1.8.13/config . # didn't even have to do this
# export AUGUSTUS_CONFIG_PATH=$(pwd)/config # didn't even have to set this
funannotate test -t all
I thought augustus config dir has to be writeable, so I copied it (apparently non-fully) and thus introduced a bug.
I found my error!!! Thanks for the support! @nextgenusfs When I copied the augustus config dir, the
parametersdir wasn't transferred. This resolved it:rm -r config # cp -r $(conda info --base)/envs/funannotate-1.8.13/config . # didn't even have to do this # export AUGUSTUS_CONFIG_PATH=$(pwd)/config # didn't even have to set this funannotate test -t allI thought augustus config dir has to be writeable, so I copied it (apparently non-fully) and thus introduced a bug.
Hey so it was a problem with the augustus config dir, and it wasn't the same as ours!
If you own the conda env, you shouldn't have to do the copy of the config dir. Otherwise, as far as I can tell, users should have to copy the config out and set the AUGUSTUS_CONFIG_PATH manually.
I have the same issue with braker/braker2 for my users, so I run basically the same script as for the funannotate in terms of copying the config dir out and setting the env var for them.
Hello! I am running and setting funannotate for the first time. I could run "clean" and "sort" steps. I had already a masked version of the genomes, so I avoided that step. When I run "funannotate predict" it gets stuck in nothing happens, and files are created except for empty logfiles predict_misc predict_results, with the logfile and screen stuck in
"[Apr 07 02:29 AM]: OS: Ubuntu 20.04, 72 cores, ~ 528 GB RAM. Python: 3.8.15 [Apr 07 02:29 AM]: Running funannotate v1.8.13]"
the command I use: "funannotate predict -i genome_sort/Phaffia.fna -o genomes_predict -s "Cryptococcus neoformans" --protein_evidence $FUNANNOTATE_DB/uniprot_sprot.fasta --GENEMARK_PATH /home/jose/ProtHint/dependencies/GeneMarkES/gmes_petap.pl"
same happens if I run the test: "funannotate test -t predict --cpus 20 --debug"
These are my dependencies, I am using a previous genemark dir I had already funannotate check --show-versions:
Checking dependencies for 1.8.13
You are running Python v 3.8.15. Now checking python packages... biopython: 1.81 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.3.1 numpy: 1.24.2 pandas: 2.0.0 psutil: 5.6.7 requests: 2.28.2 scikit-learn: 1.2.2 scipy: 1.10.1 seaborn: 0.12.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/linuxhome/tmp/jose/Leva/Levas_assemblies/funannotate/funannotate_db $PASAHOME=/home/jose/miniconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/jose/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/jose/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/jose/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/jose/gmes_linux_64_4/gmes_petap.pl:/home/jose/jose2/CAT_prepare_20210107/Diamond_2.0.6:/home/jose/CAT/CAT_pack:/home/jose/miniconda3/bin:/tbb/local/bin:/home/jose/gmes_linux_64_4/gmes_petap.pl:/home/jose/jose2/CAT_prepare_20210107/Diamond_2.0.6:/home/jose/CAT/CAT_pack:/home/jose/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin All 6 environmental variables are set
Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.6 emapper.py: [31mThere was an error retrieving eggnog-mapper DB data: not a valid file "/home/jose/miniconda3/lib/python3.8/site-packages/data/eggnog.db"[0m [0mMaybe you need to run download_eggnog_data.py[0m emapper-2.1.3
ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: pigz 2.6 proteinortho: 6.2.3 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.17 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 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: gmes_petap.pl not installed
Hope you can help Best
sorry that i can't help you, my issue about funannotate still not solve, good luck to you !
------------------ 原始邮件 ------------------ 发件人: "nextgenusfs/funannotate" @.>; 发送时间: 2023年4月7日(星期五) 上午10:34 @.>; @.@.>; 主题: Re: [nextgenusfs/funannotate] test failure (Issue #852)
Hello! I am running and setting funannotate for the first time. I could run "clean" and "sort" steps. I had already a masked version of the genomes, so I avoided that step. When I run "funannotate predict" it gets stuck in nothing happens, and files are created except for empty logfiles predict_misc predict_results, with the logfile and screen stuck in
"[Apr 07 02:29 AM]: OS: Ubuntu 20.04, 72 cores, ~ 528 GB RAM. Python: 3.8.15 [Apr 07 02:29 AM]: Running funannotate v1.8.13]"
the command I use: "funannotate predict -i genome_sort/Phaffia.fna -o genomes_predict -s "Cryptococcus neoformans" --protein_evidence $FUNANNOTATE_DB/uniprot_sprot.fasta --GENEMARK_PATH /home/jose/ProtHint/dependencies/GeneMarkES/gmes_petap.pl"
same happens if I run the test: "funannotate test -t predict --cpus 20 --debug"
These are my dependencies, I am using a previous genemark dir I had already funannotate check --show-versions:
Checking dependencies for 1.8.13
You are running Python v 3.8.15. Now checking python packages... biopython: 1.81 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.3.1 numpy: 1.24.2 pandas: 2.0.0 psutil: 5.6.7 requests: 2.28.2 scikit-learn: 1.2.2 scipy: 1.10.1 seaborn: 0.12.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/linuxhome/tmp/jose/Leva/Levas_assemblies/funannotate/funannotate_db $PASAHOME=/home/jose/miniconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/jose/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/jose/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/jose/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/jose/gmes_linux_64_4/gmes_petap.pl:/home/jose/jose2/CAT_prepare_20210107/Diamond_2.0.6:/home/jose/CAT/CAT_pack:/home/jose/miniconda3/bin:/tbb/local/bin:/home/jose/gmes_linux_64_4/gmes_petap.pl:/home/jose/jose2/CAT_prepare_20210107/Diamond_2.0.6:/home/jose/CAT/CAT_pack:/home/jose/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin All 6 environmental variables are set
Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.6 emapper.py: �[31mThere was an error retrieving eggnog-mapper DB data: not a valid file "/home/jose/miniconda3/lib/python3.8/site-packages/data/eggnog.db"�[0m �[0mMaybe you need to run download_eggnog_data.py�[0m emapper-2.1.3
ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: pigz 2.6 proteinortho: 6.2.3 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.17 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 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: gmes_petap.pl not installed
Hope you can help Best
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
When I run "funannotate predict" it gets stuck in nothing happens, and files are created except for empty logfiles predict_misc predict_results, with the logfile and screen stuck in
@JoseLopezArcondo I think this behavior is from a incompatible augustus install on your system. So one of the first things that is done in the script is to check dependencies, so I think it is trying to run bam2hints from augustus to see if it is installed properly and it just gets stuck without any response. I have seen this before where it seemed like augustus was functioning properly, but the accessory scripts that come with augustus were not compiled correctly. Solution is to install either a different version of augustus or install manually.
allright, I can try that. I removed augustus package in funannotate but now it does not work. I guess it removed more stuff in the process. Is there a way to install all these at once with conda with the appropriate packages in some setting that should allways work? something like "conda install funannotate ##listOfPackagesAndVersions" ?? Best
Perhaps you can check out this official tutorial https://funannotate.readthedocs.io/en/latest/install.html
------------------ 原始邮件 ------------------ 发件人: "nextgenusfs/funannotate" @.>; 发送时间: 2023年4月10日(星期一) 晚上10:35 @.>; @.@.>; 主题: Re: [nextgenusfs/funannotate] test failure (Issue #852)
allright, I can try that. I removed augustus package in funannotate but now it does not work. I guess it removed more stuff in the process. Is there a way to install all these at once with conda with the appropriate packages, that should work? something like "conda install funannotate ##listOfPackagesAndVersions" ?? Best
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
You can see how I installed in the docker image using the Debian packages Augustus version here https://github.com/nextgenusfs/funannotate/blob/master/Dockerfile
Thanks a lot. Yes, I think this is working. I created a new mamba using augustus 3.4 and seems to be running well.
Here another issue I found while running "predict" "error: [Errno 2] No such file or directory: '/home/jose/miniconda3/envs/funannotate/opt/evidencemodeler-2.1.0/evidence_modeler.pl'" Is it some configuration issue?
Current content in that folder is: EVidenceModeler EvmUtils PerlLib plugins
Best
Ugh.. Looks like EVM v2.0 changed its executable name. You an fix downgrade evidence modeler < v2.0
thanks, I think that solves it. Now I have this issue as well, these types of errors appear all the time.. "Error: In sequence scaffold_1_45659-49698: One CDS exon does not begin properly after the previous CDS exon.602 >= 600 GBProcessor::getGeneList(): Intron has non-positive length. Encountered error after reading 0 annotations."
I am using only genome data of different fungi from Basidiomycota, and using "cryptococcus" to predict, because it's I think the closest in the pre-trained. Could this error be related? best