nextgenusfs
commented
2 years ago Weird, apparently adding local-lib caused the glimmerhmm perl error... I think the current is fixed, can you confirm fixed?
$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
nextgenusfs/funannotate latest 23522b878a09 4 hours ago 10.8GB$ ./funannotate_dev/funannotate-docker test -t predict annotate --cpus 6
#########################################################
Running `funannotate predict` unit testing
CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 6 --species Awesome testicus
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[Mar 27 02:25 AM]: OS: Debian GNU/Linux 10, 4 cores, ~ 8 GB RAM. Python: 3.8.12
[Mar 27 02:25 AM]: Running funannotate v1.8.10
[Mar 27 02:25 AM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[Mar 27 02:25 AM]: Skipping CodingQuarry as no --rna_bam passed
[Mar 27 02:25 AM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus pretrained
glimmerhmm busco
snap busco
[Mar 27 02:25 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Mar 27 02:25 AM]: Genome loaded: 6 scaffolds; 3,776,588 bp; 19.75% repeats masked
[Mar 27 02:25 AM]: Mapping 1,065 proteins to genome using diamond and exonerate
[Mar 27 02:25 AM]: Found 1,505 preliminary alignments with diamond in 0:00:02 --> generated FASTA files for exonerate in 0:00:00
[Mar 27 02:26 AM]: Exonerate finished in 0:00:32: found 1,270 alignments
[Mar 27 02:26 AM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Mar 27 02:40 AM]: 373 valid BUSCO predictions found, validating protein sequences
[Mar 27 02:41 AM]: 370 BUSCO predictions validated
[Mar 27 02:41 AM]: Running Augustus gene prediction using saccharomyces parameters
[Mar 27 02:44 AM]: 1,485 predictions from Augustus
[Mar 27 02:44 AM]: Pulling out high quality Augustus predictions
[Mar 27 02:44 AM]: Found 371 high quality predictions from Augustus (>90% exon evidence)
[Mar 27 02:44 AM]: Running SNAP gene prediction, using training data: annotate/predict_misc/busco.final.gff3
[Mar 27 02:47 AM]: 1,508 predictions from SNAP
[Mar 27 02:47 AM]: Running GlimmerHMM gene prediction, using training data: annotate/predict_misc/busco.final.gff3
[Mar 27 02:50 AM]: 1,774 predictions from GlimmerHMM
[Mar 27 02:50 AM]: Summary of gene models passed to EVM (weights):
Source Weight Count
Augustus 1 1325
Augustus HiQ 2 372
GlimmerHMM 1 1774
snap 1 1508
Total - 4979
[Mar 27 02:50 AM]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval
[Mar 27 02:59 AM]: Converting to GFF3 and collecting all EVM results
[Mar 27 02:59 AM]: 1,688 total gene models from EVM
[Mar 27 02:59 AM]: Generating protein fasta files from 1,688 EVM models
[Mar 27 02:59 AM]: now filtering out bad gene models (< 50 aa in length, transposable elements, etc).
[Mar 27 02:59 AM]: Found 135 gene models to remove: 0 too short; 0 span gaps; 135 transposable elements
[Mar 27 02:59 AM]: 1,553 gene models remaining
[Mar 27 02:59 AM]: Predicting tRNAs
[Mar 27 02:59 AM]: 112 tRNAscan models are valid (non-overlapping)
[Mar 27 02:59 AM]: Generating GenBank tbl annotation file
[Mar 27 02:59 AM]: Collecting final annotation files for 1,665 total gene models
[Mar 27 02:59 AM]: Converting to final Genbank format
[Mar 27 03:00 AM]: Funannotate predict is finished, output files are in the annotate/predict_results folder
[Mar 27 03:00 AM]: Your next step might be functional annotation, suggested commands:
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Run InterProScan (manual install):
funannotate iprscan -i annotate -c 6
Run antiSMASH (optional):
funannotate remote -i annotate -m antismash -e youremail@server.edu
Annotate Genome:
funannotate annotate -i annotate --cpus 6 --sbt yourSBTfile.txt
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[Mar 27 03:00 AM]: Training parameters file saved: annotate/predict_results/saccharomyces.parameters.json
[Mar 27 03:00 AM]: Add species parameters to database:
funannotate species -s saccharomyces -a annotate/predict_results/saccharomyces.parameters.json
#########################################################
SUCCESS: `funannotate predict` test complete.
#########################################################
Shellfishgene
tjhinet
Are you using the latest release? Yes, from Docker:
singularity pull funannotate.sif docker://nextgenusfs/funannotate:latestDescribe the bug I just ran the funnannotate test using Singularity, but
trainGlimmerHMMfails due to the Getop/Std Perl module missing. RunningtrainGlimmerHMMdirectly from the shell inside the container also results in this error. I also tried installing GlimmerHMM from conda to check if the error comes from the conda recipe for Glimmer, but the following works fine here:So the Conda recipe seems fine?
What command did you issue?
singularity exec docker://nextgenusfs/funannotate funannotate test -t all --cpus 4orsingularity exec funannotate.sif trainGlimmerHMMLogfiles
OS/Install Information