ruthpg
commented
7 months ago how did you solve this issue? @nextgenusfs I ran into the same issue, and in addition I was getting quite some other errors, some look like:
FUN_029468 Feature overlapped by 2 identical-length genes but has no cross-reference
FUN_029469 Feature overlapped by 2 identical-length genes but has no cross-reference
FUN_029502 Feature begins or ends in gap starting at 1627056
FUN_029528 CDS not contained within cross-referenced mRNAThen if I look into the tbl file, these two genes indeed have identical length and do not cross reference each other, how should this be fixed?:
686279 688092 gene
locus_tag FUN_029468
686279 686935 mRNA
687021 688092
product hypothetical protein
transcript_id gnl|ncbi|FUN_029468-T1_mrna
protein_id gnl|ncbi|FUN_029468-T1
686582 686935 CDS
687021 687803
codon_start 1
product hypothetical protein
transcript_id gnl|ncbi|FUN_029468-T1_mrna
protein_id gnl|ncbi|FUN_029468-T1
686279 686935 mRNA
687021 687376
687540 688092
product hypothetical protein
transcript_id gnl|ncbi|FUN_029468-T2_mrna
protein_id gnl|ncbi|FUN_029468-T2
686308 686935 CDS
687021 687376
687540 687803
codon_start 1
product hypothetical protein
transcript_id gnl|ncbi|FUN_029468-T2_mrna
protein_id gnl|ncbi|FUN_029468-T2
686279 687376 mRNA
687540 688092
product hypothetical protein
transcript_id gnl|ncbi|FUN_029468-T3_mrna
protein_id gnl|ncbi|FUN_029468-T3
686308 687376 CDS
687540 687688
codon_start 1
product hypothetical protein
transcript_id gnl|ncbi|FUN_029468-T3_mrna
protein_id gnl|ncbi|FUN_029468-T3686279 688092 gene
locus_tag FUN_029469
686279 688092 mRNA
product hypothetical protein
transcript_id gnl|ncbi|FUN_029469-T1_mrna
protein_id gnl|ncbi|FUN_029469-T1
686308 687426 CDS
codon_start 1
product hypothetical protein
transcript_id gnl|ncbi|FUN_029469-T1_mrna
protein_id gnl|ncbi|FUN_029469-T1for this gene it complains that start or ends in a gap starting at 1627056:
1627057 1625448 gene
locus_tag FUN_029502
1627057 1626623 mRNA
1626464 1626390
1626323 1626248
1626122 1625448
product hypothetical protein
transcript_id gnl|ncbi|FUN_029502-T1_mrna
protein_id gnl|ncbi|FUN_029502-T1
1626732 1626623 CDS
1626464 1626390
1626323 1626248
1626124 1625822
codon_start 1
product hypothetical protein
transcript_id gnl|ncbi|FUN_029502-T1_mrna
protein_id gnl|ncbi|FUN_029502-T1And for this one it says "CDS not contained within cross-referenced mRNA", but I cannot really see what is wrong with it...
2522815 2523725 gene
locus_tag FUN_029528
2522815 2523725 mRNA
product hypothetical protein
transcript_id gnl|ncbi|FUN_029528-T1_mrna
protein_id gnl|ncbi|FUN_029528-T1
2522901 2523377 CDS
codon_start 1
product hypothetical protein
transcript_id gnl|ncbi|FUN_029528-T1_mrna
protein_id gnl|ncbi|FUN_029528-T1Emiliania_huxleyi_CCMP1516.models-need-fixing.txt Emiliania_huxleyi_CCMP1516.zip I'd appreciate any help to be able to finish this annotation :)
Are you using the latest release? I'm using the latest version available in docker (v1.8.15) Describe the bug After I ran funannotate update, I got a message about several gene models that need fixing:
When I checked the tbl file, I indeed saw that genes FUN_010869 and FUN_010870 overlap in length, but have different CDSs:
How should I fix the file? Should I move mRNA and CDS features from FUN_010870 to FUN_010869, and remove FUN_010870? Would that work? Thank you!
What command did you issue? singularity run ../singularity/funannotate.sif funannotate update -i analysis_and_temp_files/06_annotate_lecanoro/Xp_jgi_pred/ --cpus 28
Logfiles
OS/Install Information
funannotate check --show-versionsYou are running Perl v b'5.026002'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.855 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.29 local::lib: 2.000024 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed
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... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.2 bamtools: bamtools 2.5.2 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.6 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 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.0.16 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 40 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: pslCDnaFilter not installed
ERROR: signalp not installed