also have error in funannotate predict and annotate

gengce commented 5 years ago

(python2) [root@localgc 1Genome_quast_introduction]# funannotate test -t annotate ######################################################### Running `funannotate annotate` unit testing Downloading: https://osf.io/97pyn/download?version=1 Bytes: 341476 CMD: funannotate annotate --genbank Genome_one.gbk -o annotate --cpus 2 --iprscan genome_one.iprscan.xml --eggnog genome_one.emapper.annotations #########################################################

[12:10 PM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [12:10 PM]: Running funannotate v1.5.3 [12:10 PM]: Database files not found in /home/funannotate/FunDB, run funannotate database and/or funannotate setup ######################################################### ERROR: funannotate annotate test failed - check logfiles #########################################################

(python2) [root@localgc 1Genome_quast_introduction]# funannotate test -t annotate -check logfiles usage: funannotate-test.py [-h] -t {all,clean,mask,predict,annotate,busco,rna-seq,compare} [{all,clean,mask,predict,annotate,busco,rna-seq,compare} ...] [--cpus CPUS] funannotate-test.py: error: unrecognized arguments: -check logfiles (python2) [root@localgc 1Genome_quast_introduction]# funannotate test -t predict ######################################################### Running `funannotate predict` unit testing Downloading: https://osf.io/te2pf/download?version=1 Bytes: 1489808 CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 2 --species Awesome testicus #########################################################

[12:11 PM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [12:11 PM]: Running funannotate v1.5.3 [12:11 PM]: Augustus training set for saccharomyces already exists. To re-train provide unique --augustus_species argument [12:11 PM]: AUGUSTUS (3.2.3) detected, version seems to be compatible with BRAKER and BUSCO [12:11 PM]: Loading genome assembly and parsing soft-masked repetitive sequences [12:11 PM]: Genome loaded: 6 scaffolds; 3,776,588 bp; 19.75% repeats masked [12:11 PM]: Mapping proteins to genome using Diamond blastx/Exonerate [12:11 PM]: Using 1,065 proteins as queries [12:11 PM]: Running Diamond pre-filter search [12:11 PM]: Found 1,774 preliminary alignments [12:12 PM]: Exonerate finished: found 1,341 alignments Traceback (most recent call last): File "/home/funannotate/bin/funannotate-p2g.py", line 275, in lib.SafeRemove(tmpdir) File "/home/funannotate/lib/library.py", line 686, in SafeRemove shutil.rmtree(input) File "/root/miniconda3/envs/python2/lib/python2.7/shutil.py", line 270, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/root/miniconda3/envs/python2/lib/python2.7/shutil.py", line 268, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: 'p2g_19893' Traceback (most recent call last): File "/home/funannotate/bin/funannotate-predict.py", line 654, in lib.runSubprocess5(cmd, '.', lib.log, allhintstmp_sort, hints_all) File "/home/funannotate/lib/library.py", line 732, in runSubprocess5 proc = subprocess.Popen(cmd, cwd=dir, stdin=infile, stdout=out, stderr=subprocess.PIPE) File "/root/miniconda3/envs/python2/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/root/miniconda3/envs/python2/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ######################################################### Traceback (most recent call last): File "/home/funannotate/bin/funannotate-test.py", line 334, in runPredictTest() File "/home/funannotate/bin/funannotate-test.py", line 168, in runPredictTest assert 1500 <= countGFFgenes(os.path.join(tmpdir, 'annotate', 'predict_results', 'Awesome_testicus.gff3')) <= 1700 File "/home/funannotate/bin/funannotate-test.py", line 58, in countGFFgenes with open(input, 'rU') as f: IOError: [Errno 2] No such file or directory: 'test-predict_19800/annotate/predict_results/Awesome_testicus.gff3'

the error told me :"Database files not found in /home/funannotate/FunDB, run funannotate database and/or funannotate setup",But indeed I have setup database (python2) [root@localgc 1Genome_quast_introduction]# funannotate setup -u -b fungi -d /home/funannotate/FunDB -u

[09:57 AM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [09:57 AM]: Running funannotate v1.5.3 [09:57 AM]: Database location: /home/funannotate/FunDB [09:57 AM]: Checking for newer versions of database files [09:58 AM]: merops database is current. [09:58 AM]: MEROPS Database: version=12.0 date=2017-10-04 records=4,968 [09:58 AM]: uniprot-release database is current. [09:58 AM]: UniProtKB Database: version=2019_02 date=2019-02-13 records=559,228 [10:00 AM]: dbCAN database is current. [10:00 AM]: dbCAN Database: version=7.0 date=2018-08-25 records=607 [10:00 AM]: pfam-log database is current. [10:00 AM]: Pfam Database: version=32.0 date=2018-08 records=17,929 [10:00 AM]: repeats database is current. [10:00 AM]: Repeat Database: version=1.0 date=2019-03-25 records=11,950 [10:02 AM]: go-obo database is out of date, updating. [10:02 AM]: Downloading GO Ontology database [10:02 AM]: Downloading: http://purl.obolibrary.org/obo/go.obo Bytes: 34091323 [10:03 AM]: GO ontology version=2019-03-19 date=2019-03-19 records=47,362 [10:04 AM]: mibig database is current. [10:04 AM]: MiBIG Database: version=1.4 date=2019-03-25 records=31,023 [10:07 AM]: interpro database is current. [10:07 AM]: InterProScan XML: version=73.0 date=2019-03-21 records=36,702 [10:07 AM]: outgroups not found in database [10:07 AM]: Downloading pre-computed BUSCO outgroups [10:07 AM]: Downloading: https://osf.io/r9sne/download?version=1 Bytes: 2374032 [10:07 AM]: BUSCO outgroups: version=1.0 date=2019-03-28 records=8 [10:07 AM]: gene2product database is current. [10:07 AM]: Gene2Product: version=1.31 date=2019-02-20 records=26,139 [10:07 AM]: Downloading busco models: fungi [10:07 AM]: Funannoate setup complete. Add this to ~/.bash_profile or ~/.bash_aliases:

export FUNANNOTATE_DB=/home/funannotate/FunDB

(python2) [root@localgc 1Genome_quast_introduction]# export FUNANNOTATE_DB=/home/funannotate/FunDB (python2) [root@localgc 1Genome_quast_introduction]# funannotate database

Funannotate Databases currently installed:

Database Type Version Date Num_Records Md5checksum
pfam hmmer3 32.0 2018-08 17929 de7496fad69c1040fd74db1cb5eef0fc gene2product text 1.31 2019-02-20 26139 fd87019053c59ed6b4162e0ca5633c89 interpro xml 73.0 2019-03-21 36702 9e1b0aeb614451d08ca4e3688b844c64 dbCAN hmmer3 7.0 2018-08-25 607 51c724c1f9ac45687f08d0faa689ed58 busco_outgroups outgroups 1.0 2019-03-28 8 6795b1d4545850a4226829c7ae8ef058 merops diamond 12.0 2017-10-04 4968 d923f0177c6d27c3d2886c705347adc0 mibig diamond 1.4 2019-03-25 31023 118f2c11edde36c81bdea030a0228492 uniprot diamond 2019_02 2019-02-13 559228 7b42b43b6a9cc28f2424d2fa73ae4852 go text 2019-03-19 2019-03-19 47362 00575e6917279fc76cfd1b076406d1ac repeats diamond 1.0 2019-03-25 11950 4e8cafc3eea47ec7ba505bb1e3465d21

To update a database type: funannotate setup -i DBNAME -d /home/funannotate/FunDB --force

nextgenusfs commented 5 years ago

What version of diamond and version of exonerate? Would be helpful to post output of funannotate check —show-versions

gengce commented 5 years ago

(python2) [root@localgc annotatation]# funannotate annotate --gff comp_genemark.gff3 --fasta coemp.fa -s "Coleophoma empetri" -o FUNcolemp

[02:44 PM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [02:44 PM]: Running funannotate v1.5.3 [02:44 PM]: Database files not found in /home/funannotate/FunDB, run funannotate database and/or funannotate setup (python2) [root@localgc annotatation]# funannotate database

Funannotate Databases currently installed:

Database Type Version Date Num_Records Md5checksum
pfam hmmer3 32.0 2018-08 17929 de7496fad69c1040fd74db1cb5eef0fc gene2product text 1.32 2019-03-27 26175 3278dd8de7513e0ba2d6f3f3f1e0b1fd interpro xml 73.0 2019-03-21 36702 9e1b0aeb614451d08ca4e3688b844c64 dbCAN hmmer3 7.0 2018-08-25 607 51c724c1f9ac45687f08d0faa689ed58 busco_outgroups outgroups 1.0 2019-03-29 8 6795b1d4545850a4226829c7ae8ef058 merops diamond 12.0 2017-10-04 4968 d923f0177c6d27c3d2886c705347adc0 mibig diamond 1.4 2019-03-25 31023 118f2c11edde36c81bdea030a0228492 uniprot diamond 2019_02 2019-02-13 559228 7b42b43b6a9cc28f2424d2fa73ae4852 go text 2019-03-19 2019-03-19 47362 00575e6917279fc76cfd1b076406d1ac repeats diamond 1.0 2019-03-25 11950 4e8cafc3eea47ec7ba505bb1e3465d21

To update a database type: funannotate setup -i DBNAME -d /home/funannotate/FunDB --force

(python2) [root@localgc annotatation]# funannotate check --vesion

^[[AChecking dependencies for funannotate v1.5.3

You are running Python v 2.7.15. Now checking python packages... All 11 python packages installed

You are running Perl v 5.026002. Now checking perl modules... All 27 Perl modules installed

Checking external dependencies... All 32 external dependencies are installed

Checking Environmental Variables... All 7 environmental variables are set

gengce commented 5 years ago

I am so sorry for not show the dependencies versions (python2) [root@localgc annotatation]# funannotate check --show-versions

Checking dependencies for funannotate v1.5.3

You are running Python v 2.7.15. Now checking python packages... biopython: 1.72 goatools: 0.8.12 matplotlib: 2.2.3 natsort: 6.0.0 numpy: 1.16.2 pandas: 0.24.2 psutil: 5.6.1 requests: 2.21.0 scikit-learn: 0.20.3 scipy: 1.2.1 seaborn: 0.9.0 All 11 python packages installed

You are running Perl v 5.026002. Now checking perl modules... Bio::Perl: 1.007002 Carp: 1.50 Clone: 0.41 DBD::SQLite: 1.60 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.843 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: 6.37 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.11 Text::Soundex: 3.05 Thread::Queue: 3.13 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.27 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking external dependencies... CodingQuarry: 2.0 RepeatMasker: RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ RepeatModeler: RepeatModeler 1.0.11 Trinity: 2.5.1 augustus: 3.2.3 bamtools: bamtools 2.4.1 bedtools: bedtools v2.27.1 blat: BLAT v36 diamond: diamond 0.9.24 emapper.py: emapper-1.0.3-3-g3e22728 ete3: 3.1.1 exonerate: exonerate 2.4.0 fasta: no way to determine gmap: 2018-07-04 gmes_petap.pl: 4.38 hisat2: 2.1.0 hmmscan: HMMER 3.2.1 (June 2018) hmmsearch: HMMER 3.2.1 (June 2018) java: 1.8.0_121 kallisto: 0.44.0 mafft: v7.427 (2019/Mar/24) makeblastdb: makeblastdb 2.6.0+ minimap2: 2.16-r922 nucmer: 3.1 pslCDnaFilter: no way to determine rmblastn: rmblastn 2.6.0+ samtools: samtools 1.9 stringtie: 1.3.5 tRNAscan-SE: 2.0.2 (February 2019) tbl2asn: unknown, likely 25.3 tblastn: tblastn 2.6.0+ trimal: trimAl v1.4.rev15 build[2013-12-17] All 32 external dependencies are installed

Checking Environmental Variables... $FUNANNOTATE_DB=/home/funannotate/FunDB $PASAHOME=/root/PASApipeline $TRINITYHOME=/root/Trinity $EVM_HOME=/root/evidencemodeler $AUGUSTUS_CONFIG_PATH=/root/miniconda3/pkgs/augustus-3.2.3-boost1.60_0/config $GENEMARK_PATH=/opt/biosoft/gm_et_linux_64/gmes_petap $BAMTOOLS_PATH=/root/bamtools All 7 environmental variables are set

nextgenusfs commented 5 years ago

Hmmm, nothing seems out of place... What OS and version? Are you on a mounted file structure? Could you also list the files in the funannotate database location, ie ls -l $FUNANNOTATE_DB

gengce commented 5 years ago

Every time I must export the DB location again. My emapper database base have been moved to other place, have the effect on the annotate ? (python2) [root@localgc FunDB]# export FUNANNOTATE_DB=/home/funannotate/FunDB \

export PASAHOME=/root/PASApipeline \ export TRINITYHOME=/root/Trinity \ export EVM_HOME=/root/evidencemodeler \ export AUGUSTUS_CONFIG_PATH=/root/miniconda3/pkgs/augustus-3.2.3-boost1.60_0/config \ export GENEMARK_PATH=/opt/biosoft/gm_et_linux_64/gmes_petap \ export BAMTOOLS_PATH=/root/bamtools (python2) [root@localgc FunDB]# ls -l $FUNANNOTATE_DB总用量 2313824 drwxr-xr-x. 5 1046 1200 147 2月 14 2017 actinopterygii drwxr-xr-x. 5 1046 1200 147 11月 18 2016 alveolata_stramenophiles drwxr-xr-x. 5 1046 1200 147 11月 1 2016 arthropoda drwxr-xr-x. 5 1046 1200 147 2月 13 2017 ascomycota drwxr-xr-x. 5 1046 1200 147 2月 13 2017 aves drwxr-xr-x. 5 1046 1200 147 2月 13 2017 basidiomycota -rwxrwxrwx. 1 root root 2374032 3月 29 14:34 busco_outgroups.tar.gz -rwxrwxrwx. 1 root root 6082 3月 28 14:57 dbCAN.changelog.txt -rwxrwxrwx. 1 root root 59480 3月 28 14:57 dbCAN-fam-HMMs.txt -rwxrwxrwx. 1 root root 87670624 3月 28 14:57 dbCAN.hmm -rwxrwxrwx. 1 root root 26459 7月 4 2018 dbCAN.hmm.h3i drwxrwxrwx. 5 root root 147 2月 13 2017 dikarya drwxr-xr-x. 5 1046 1200 147 2月 13 2017 diptera drwxr-xr-x. 5 1046 1200 147 2月 13 2017 endopterygota drwxr-xr-x. 5 1046 1200 147 2月 13 2017 euarchontoglires drwxr-xr-x. 5 1046 1200 147 11月 2 2016 eukaryota drwxr-xr-x. 5 1046 1200 147 2月 13 2017 eurotiomycetes -rwxrwxrwx. 1 root root 1068 3月 29 14:34 funannotate-db-info.txt -rw-r--r--. 1 501 games 11017103 3月 2 2016 funannotate.repeat.proteins.fa -rwxrwxrwx. 1 root root 11017079 3月 25 18:02 funannotate.repeats.reformat.fa drwxr-xr-x. 5 1046 1200 147 2月 13 2017 fungi -rwxrwxrwx. 1 root root 34091323 3月 28 10:03 go.obo drwxr-xr-x. 3 root root 21 3月 26 12:29 hmmdb_levels drwxr-xr-x. 5 1046 1200 147 2月 13 2017 hymenoptera drwxr-xr-x. 5 1046 1200 147 2月 13 2017 insecta -rw-r--r--. 1 root root 168332787 3月 28 09:26 interpro.xml drwxr-xr-x. 3 1046 1200 18 2月 13 2017 laurasiatheria drwxr-xr-x. 5 1046 1200 147 2月 13 2017 mammalia -rwxrwxrwx. 1 root root 1434038 3月 25 18:04 merops.dmnd -rwxrwxrwx. 1 root root 1372931 3月 25 18:04 merops.formatted.fa -rwxrwxrwx. 1 root root 1942655 3月 25 18:04 merops_scan.lib drwxr-xr-x. 5 1046 1200 182 2月 13 2017 metazoa -rwxrwxrwx. 1 root root 21740850 3月 25 17:57 mibig.dmnd -rwxrwxrwx. 1 root root 21244378 3月 25 17:57 mibig.fa drwxr-xr-x. 5 1046 1200 147 2月 13 2017 microsporidia -rwxrwxrwx. 1 root root 1037981 3月 28 15:00 ncbi_cleaned_gene_products.txt drwxr-xr-x. 5 1046 1200 147 2月 13 2017 nematoda drwxr-xr-x. 2 501 games 4096 12月 5 2016 outgroups drwxr-xr-x. 3 1046 1200 18 2月 13 2017 pezizomycotina -rw-r--r--. 1 root root 1041991 3月 25 17:14 Pfam-A.clans.tsv -rw-r--r--. 1 root root 1434541235 3月 25 17:13 Pfam-A.hmm -rwxrwxrwx. 1 root root 1153233 7月 4 2018 Pfam-A.hmm.h3i -rw-r--r--. 1 root root 111 3月 25 17:14 Pfam.version drwxr-xr-x. 5 1046 1200 147 11月 18 2016 protists -rwxrwxrwx. 1 root root 11090223 3月 25 18:02 repeats.dmnd drwxr-xr-x. 5 1046 1200 147 2月 13 2017 saccharomycetales drwxr-xr-x. 5 1046 1200 147 2月 13 2017 saccharomycetes drwxr-xr-x. 5 1501 1200 147 2月 13 2017 sordariomycetes drwxr-xr-x. 5 1046 1200 147 2月 13 2017 tetrapoda -rwxrwxrwx. 1 root root 281991405 3月 25 18:08 uniprot.dmnd -rwxrwxrwx. 1 root root 151 3月 25 18:08 uniprot.release-date.txt -rw-r--r--. 1 root root 276112349 3月 25 18:07 uniprot_sprot.fasta drwxr-xr-x. 5 1046 1200 147 2月 13 2017 vertebrata My OS version: (python2) [root@localgc FunDB]# cat /etc/os-release NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

(python2) [root@localgc FunDB]# lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.5.1804 (Core) Release: 7.5.1804 Codename: Core

gengce commented 5 years ago

annotate problem still exsit, and I laso moved the files that need be annotated to root files. (python2) [root@localgc COEMP]# pwd /root/COEMP (python2) [root@localgc COEMP]# ls coemp.fa comp_genemark.gff3 funannotate-annotate.log funannotate-setup.log (python2) [root@localgc COEMP]# funannotate annotate --gff comp_genemark.gff3 --fasta coemp.fa -s "Coleophoma empetri" -o FUNcolemp

[10:33 AM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [10:33 AM]: Running funannotate v1.5.3 [10:33 AM]: Database files not found in /home/funannotate/FunDB, run funannotate database and/or funannotate setup (python2) [root@localgc COEMP]# funannotate database

Funannotate Databases currently installed:

Database Type Version Date Num_Records Md5checksum
pfam hmmer3 32.0 2018-08 17929 de7496fad69c1040fd74db1cb5eef0fc gene2product text 1.32 2019-03-27 26175 3278dd8de7513e0ba2d6f3f3f1e0b1fd interpro xml 73.0 2019-03-21 36702 9e1b0aeb614451d08ca4e3688b844c64 dbCAN hmmer3 7.0 2018-08-25 607 51c724c1f9ac45687f08d0faa689ed58 busco_outgroups outgroups 1.0 2019-03-29 8 6795b1d4545850a4226829c7ae8ef058 merops diamond 12.0 2017-10-04 4968 d923f0177c6d27c3d2886c705347adc0 mibig diamond 1.4 2019-03-25 31023 118f2c11edde36c81bdea030a0228492 uniprot diamond 2019_02 2019-02-13 559228 7b42b43b6a9cc28f2424d2fa73ae4852 go text 2019-03-19 2019-03-19 47362 00575e6917279fc76cfd1b076406d1ac repeats diamond 1.0 2019-03-25 11950 4e8cafc3eea47ec7ba505bb1e3465d21

To update a database type: funannotate setup -i DBNAME -d /home/funannotate/FunDB --force

(python2) [root@localgc COEMP]# funannotate setup -d /home/funannotate/FunDB -b fungi

[10:33 AM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [10:33 AM]: Running funannotate v1.5.3 [10:33 AM]: Database location: /home/funannotate/FunDB [10:33 AM]: MEROPS Database: version=12.0 date=2017-10-04 records=4,968 [10:33 AM]: UniProtKB Database: version=2019_02 date=2019-02-13 records=559,228 [10:33 AM]: dbCAN Database: version=7.0 date=2018-08-25 records=607 [10:33 AM]: Pfam Database: version=32.0 date=2018-08 records=17,929 [10:33 AM]: Repeat Database: version=1.0 date=2019-03-25 records=11,950 [10:33 AM]: GO ontology version=2019-03-19 date=2019-03-19 records=47,362 [10:33 AM]: MiBIG Database: version=1.4 date=2019-03-25 records=31,023 [10:33 AM]: InterProScan XML: version=73.0 date=2019-03-21 records=36,702 [10:33 AM]: BUSCO outgroups: version=1.0 date=2019-03-29 records=8 [10:33 AM]: Gene2Product: version=1.32 date=2019-03-27 records=26,175 [10:33 AM]: Downloading busco models: fungi [10:33 AM]: Funannoate setup complete. Add this to ~/.bash_profile or ~/.bash_aliases:

export FUNANNOTATE_DB=/home/funannotate/FunDB

(python2) [root@localgc COEMP]# funannotate annotate --gff comp_genemark.gff3 --fasta coemp.fa -s "Coleophoma empetri" -o FUNcolemp

[10:33 AM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.15 [10:33 AM]: Running funannotate v1.5.3 [10:33 AM]: Database files not found in /home/funannotate/FunDB, run funannotate database and/or funannotate setup (python2) [root@localgc COEMP]#

gengce commented 5 years ago

after rerun the funannotate setup script the database is working, thank you very much for this fantastic software. a small suggestion: can we set the gene "product name" is not the product="hypothetical protein" in the annotate GBK format file?

nextgenusfs commented 5 years ago

Those that can be annotated will get a description for the product name, the naming requires a gene name in order to be in compliance with NCBI submission requirements. So the short answer is you can add whatever you want manually using custom annotations, but more than likely those won’t pass NCBI submission. I’ve tried to pull as many as possible.

gengce commented 5 years ago

Hi, thank you for your answer, I still do not know how to fix the product name with the file in folder annotate_misc, my command is: (python2) [root@localgc COEMP]# funannotate annotate --gff comp_genemark.gff3 --fasta coemp.fa --eggnog coemp_protein.faa.emapper.annotations --iprscan iprscan.xml -s "Coleophoma empetri" --fix annotations.genes-products.txt -o FUNcolemp but the product name in my GBK file still hypothetical protein

nextgenusfs / funannotate