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Docker container for the funannotate genome annotation pipeline

Dockerfile 28.94% Perl 4.14% Roff 66.92%
comparative-genomics genome-annotation ncbi-submission

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funannotate-docker's Issues

RepeatMasker Missing for docker

funannotate-docker mask -i DNA_clean_sort.fa -m repeatmasker -s Viridiplantae -l ../../Database/Libraries/RMRBSeqs.embl
#ERROR
[Oct 09 01:03 PM]: OS: Debian GNU/Linux 10, 80 cores, ~ 264 GB RAM. Python: 3.8.12
[Oct 09 01:03 PM]: Running funanotate v1.8.16
[Oct 09 01:03 PM]: Missing Dependencies: RepeatMasker. Please install missing dependencies and re-run script

how can I used repeatmasker after docker

ERROR in funannotate setup

hello,
I am start to build the four programs in funannotate-docker, and I have two directories /database/ and /external/ in /data/. And gm_et_linux_64 (file) , signalp-4.1(directory) and interproscan-5.46-81.0(directory) in external and change the signalp script.

Firstly, I use docker run --rm -it -v $PWD/database:/root/database -v $PWD/external:/data/external -v $PWD:/data -w /data --entrypoint /bin/bash reslp/funannotate:latest to inside the container.
Then set the FUNANNOTATE_DB environment variable export FUNANNOTATE_DB=/root/database
When i use the command "funannotate setup -i all -f",there is an error,
I want to use a command like this funannotate predict -i mygenome.fa -o output_folder -s "Aspergillus nidulans" --pasa_gff mypasamodels.gff3:8 --other_gff prediction1.gff3:5 prediction2.gff3:1

ERROR：

-------------------------------------------------------
[07:41 PM]: OS: linux2, 112 cores, ~ 1056 GB RAM. Python: 2.7.17
[07:41 PM]: Running 1.7.4
[07:41 PM]: Database location: /root/database
[07:41 PM]: Parsing Augustus pre-trained species and porting to funannotate
Traceback (most recent call last):
  File "/usr/local/bin/funannotate", line 660, in <module>
    main()
  File "/usr/local/bin/funannotate", line 650, in main
    mod.main(arguments)
  File "/usr/local/lib/python2.7/dist-packages/funannotate/setupDB.py", line 652, in main
    meropsDB(DatabaseInfo, args.force, args=args)
  File "/usr/local/lib/python2.7/dist-packages/funannotate/setupDB.py", line 132, in meropsDB
    type, name, version, date, records, checksum = info.get('merops')
TypeError: 'NoneType' object is not iterable

setupDB.py seems not work, but i didn't know how to fix ,could you help me？

IOError: [Errno 2] No such file or directory: 'p2g_18546/diamond.matches.tab'

Hello,

I am trying to run funannotate (version 1.7.4) through docker on a CentOS Linux 7. I get the following error:
"IOError: [Errno 2] No such file or directory: 'p2g_18546/diamond.matches.tab"

docker run --rm -it -v $(pwd):/data reslp/funannotate:1.7.4 predict -i JU1783-k35_Gapclosed_v1.fa.masked.cleanfun.sorted --species "Rhabditis sp. JU1783" --transcript_evidence Trinity.fasta.clean --rna_bam JU1783-RNA-reads-aln-sortedgenome.bam --protein_evidence metazoa-and-Arh-proteins.fasta --pasa_gff sample_mydb_pasa.sqlite.valid_gmap_alignments.gff3 --organism other --ploidy 2  --busco_db nematoda --strain JU1783 -o JU1783-funannotate1
-------------------------------------------------------
[01:04 PM]: OS: linux2, 24 cores, ~ 132 GB RAM. Python: 2.7.17
[01:04 PM]: Running funannotate v1.7.4
[01:04 PM]: Parsed training data, run ab-initio gene predictors as follows:
  Program        Training-Method
  augustus       pasa
  codingquarry   rna-bam
  glimmerhmm     pasa
  snap           pasa
[01:04 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[01:04 PM]: Genome loaded: 3,083 scaffolds; 58,291,147 bp; 17.03% repeats masked
[01:04 PM]: Existing transcript alignments found: JU1783-funannotate1/predict_misc/transcript_alignments.gff3
[01:04 PM]: Existing RNA-seq BAM hints found: JU1783-funannotate1/predict_misc/hints.BAM.gff
[01:07 PM]: Mapping 8,255,650 proteins to genome using diamond and exonerate
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/funannotate/aux_scripts/funannotate-p2g.py", line 266, in <module>
    Hits = parseDiamond(BlastResult)
  File "/usr/local/lib/python2.7/dist-packages/funannotate/aux_scripts/funannotate-p2g.py", line 107, in parseDiamond
    with open(blastresult, 'rU') as input:
IOError: [Errno 2] No such file or directory: 'p2g_18546/diamond.matches.tab'
Traceback (most recent call last):
  File "/usr/local/bin/funannotate", line 660, in <module>
    main()
  File "/usr/local/bin/funannotate", line 650, in main
    mod.main(arguments)
  File "/usr/local/lib/python2.7/dist-packages/funannotate/predict.py", line 951, in main
    lib.exonerate2hints(Exonerate, hintsP)
  File "/usr/local/lib/python2.7/dist-packages/funannotate/library.py", line 3315, in exonerate2hints
    with open(file, 'r') as input:
IOError: [Errno 2] No such file or directory: '/data/JU1783-funannotate1/predict_misc/protein_alignments.gff3'

Do you have any suggestions on how to fix this?

I have run the following commands (no errors) before running into the problem:

docker pull reslp/funannotate:1.7.4

docker run --rm -it -v /local/path/to/data/database:/data/database reslp/funannotate:1.7.4 setup -b nematoda

docker run --rm -it -v $(pwd):/data reslp/funannotate:1.7.4 clean -i /data/JU1783-k35_Gapclosed_v1.fa.masked -o /data/JU1783-k35_Gapclosed_v1.fa.masked.cleanfun

docker run --rm -it -v $(pwd):/data reslp/funannotate:1.7.4 sort -i /data/JU1783-k35_Gapclosed_v1.fa.masked.cleanfun -o /data/JU1783-k35_Gapclosed_v1.fa.masked.cleanfun.sorted

Any suggestion welcome!
Thanks,
Sophie

error: ete3 not installed

I use singularity to install funannotate by
singularity pull docker://reslp/funannotate:1.8.1

When funannotate check --show-versions, it showed
Traceback (most recent call last):
File "/usr/local/bin/ete3", line 6, in
from ete3.tools.ete import main
File "/usr/local/lib/python3.7/dist-packages/ete3/tools/ete.py", line 55, in
from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view,
File "/usr/local/lib/python3.7/dist-packages/ete3/tools/ete_view.py", line 48, in
from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace,
ImportError: cannot import name 'TextFace' from 'ete3' (/usr/local/lib/python3.7/dist-packages/ete3/init.py)

even I install ete3 by pip and set environmental PATH, it also happened.

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