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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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funannotate annotate error #488

Closed hao7261 closed 3 years ago

hao7261 commented 4 years ago

Hi @nextgenusfs I am getting an error I don't understand when I run funannotate annotate command. (Everything works fine from funannotate clean, sort, mask, predict and even antismash remotely.)

The error:

funannotate annotate -i '/home/ubuntu/Desktop/data/funannotate_1/g55_predict' --cpus 8

[10:26 AM]: OS: linux2, 8 cores, ~ 33 GB RAM. Python: 2.7.18 [10:26 AM]: Running 1.8.0 Traceback (most recent call last): File "/home/ubuntu/.conda/envs/fun/bin/funannotate", line 670, in main() File "/home/ubuntu/.conda/envs/fun/bin/funannotate", line 660, in main mod.main(arguments) File "/home/ubuntu/.conda/envs/fun/lib/python2.7/site-packages/funannotate/annotate.py", line 362, in main if not lib.CheckDiamondDB(os.path.join(FUNDB, 'merops.dmnd')): File "/home/ubuntu/.conda/envs/fun/lib/python2.7/site-packages/funannotate/library.py", line 566, in CheckDiamondDB for line in execute(['diamond', 'dbinfo', '-d', database]): File "/home/ubuntu/.conda/envs/fun/lib/python2.7/site-packages/funannotate/library.py", line 551, in execute raise subprocess.CalledProcessError(return_code, cmd) subprocess.CalledProcessError: Command '[u'diamond', u'dbinfo', u'-d', '/home/ubuntu/funannotate_db/merops.dmnd']' returned non-zero exit status 1

Command I ran for annotate

Funannotate annotate -i --cpus X

Funannoatate database

Funannotate Databases currently installed:

Database Type Version Date Num_Records Md5checksum
pfam hmmer3 33.1 2020-04 18259 228db640818af54066a1c23404a3ba38 gene2product text 1.64 2020-08-25 33640 aa985b947a9758cc696421923f654a27 interpro xml 81.0 2020-08-13 37821 ec10ff5e4d6f7fa4982ce00c1c6335e9 dbCAN hmmer3 9.0 2020-08-04 641 04696dfba1c3bb82ff9b72cfbb3e4a65 busco_outgroups outgroups 1.0 2020-10-01 8 6795b1d4545850a4226829c7ae8ef058 merops diamond 12.0 2017-10-04 5009 a6dd76907896708f3ca5335f58560356 mibig diamond 1.4 2020-10-01 31023 118f2c11edde36c81bdea030a0228492 uniprot diamond 2020_04 2020-08-12 563082 da5725f3aa16b176d6dcf4e7ba7c1ea1 go text 2020-09-10 2020-09-10 47243 08cf4043c53d84fcadac2be9ca7a4926 repeats diamond 1.0 2020-10-01 11950 4e8cafc3eea47ec7ba505bb1e3465d21

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

To see install BUSCO outgroups type: funannotate database --show-outgroups

To see BUSCO tree type: funannotate database --show-buscos

funannotate check --show-versions

Checking dependencies for 1.8.0

You are running Python v 2.7.18. Now checking python packages... biopython: 1.76 goatools: 1.0.6 matplotlib: 2.2.5 natsort: 6.2.0 numpy: 1.16.5 pandas: 0.24.2 psutil: 5.7.0 requests: 2.24.0 scikit-learn: 0.18.2 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: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.852 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.30 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/home/ubuntu/funannotate_db $PASAHOME=/home/ubuntu/.conda/envs/fun/opt/pasa-2.4.1 $TRINITY_HOME=/home/ubuntu/.conda/envs/fun/opt/trinity-2.8.5 $EVM_HOME=/home/ubuntu/.conda/envs/fun/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/ubuntu/.conda/envs/fun/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 v2.29.2 blat: BLAT v36 diamond: 0.8.22 emapper.py: 1.0.3 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 hmmscan: HMMER 3.1b2 (February 2015) hmmsearch: HMMER 3.1b2 (February 2015) java: 11.0.8-internal kallisto: 0.46.2 mafft: v7.471 (2020/Jul/3) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.17-r941 proteinortho: 6.0.18 pslCDnaFilter: no way to determine salmon: salmon 0.15.0 samtools: samtools 1.10 snap: 2006-07-28 stringtie: 2.1.2 tRNAscan-SE: 2.0.6 (May 2020) tantan: tantan 13 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: gmes_petap.pl not installed ERROR: hisat2 not installed ERROR: signalp not installed

How can I solve this issue?

Thank You for your attention.

nextgenusfs commented 4 years ago

What version of diamond. Looks like might be too old of a version and that cmd fails or the database doesn't exist. Try updating diamond - note that you will likely need to rerun setup with --force to reinstall databases with same version of diamond.