funannotate predict funannotate.library error when running augustus_parallel.py

Hi Jon, I’ve run into some troubles with funannotate predict. Thanks for any help!

Are you using the latest release? v.1.7.4

Describe the bug funannotate predictfails ataugustus_parallel.py`.

[05:31 AM]: Running Augustus gene prediction using trichoplax_adhaerens parameters
Traceback (most recent call last):
  `"/gpfs/ysm/project/dunn/jlm329/conda_envs/funannotate/lib/python2.7/site-packages/funannotate/aux_scripts/augustus_parallel.py", line 9, in <module>
    import funannotate.library as lib
ImportError: No module named funannotate.library
[05:31 AM]: Augustus prediction failed, check `logfiles/augustus-parallel.log`

What command did you issue?

funannotate predict -i /home/jlm329/scratch60/funannotate_scratch60/predict/trichoplax.scaffolds.fa.masked \
    --species "Trichoplax adhaerens" \
    --out fun_predict.sort \
    --rna_bam $RNA/Tad_KammSenatore.merged.sort.bam \
    --optimize_augustus \
    --transcript_evidence /home/jlm329/scratch60/funannotate_scratch60/train/fun_train.sort/training/funannotate_train.trinity-GG.fasta \
    --pasa_gff /home/jlm329/scratch60/funannotate_scratch60/train/fun_train.sort/training/funannotate_train.pasa.gff3 \
    --busco_db metazoa --max_intronlen 15000 \
    --organism other -d /home/jlm329/project/trix/funannotate_db --cpus 8 \
    --repeats2evm

Logfiles

[02:56 AM]: OS: linux2, 20 cores, ~ 131 GB RAM. Python: 2.7.15
[02:56 AM]: Running funannotate v1.7.4
[02:56 AM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[02:56 AM]: Parsed training data, run ab-initio gene predictors as follows:
[02:56 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[02:56 AM]: Genome loaded: 714 scaffolds; 92,651,896 bp; 6.99% repeats masked
[02:56 AM]: Aligning transcript evidence to genome with minimap2
[02:57 AM]: Found 61,537 alignments, wrote GFF3 and Augustus hints to file
[02:57 AM]: Extracting hints from RNA-seq BAM file using bam2hints
[03:25 AM]: Mapping 549,682 proteins to genome using diamond and exonerate
03:31 AM]: Found 212,113 preliminary alignments --> aligning with exonerate
[04:57 AM]: Exonerate finished: found 1,834 alignments
[04:57 AM]: Filtering PASA data for suitable training set
[04:58 AM]: 2,077 of 7,310 models pass training parameters
[04:58 AM]: Training Augustus using PASA gene models
[04:59 AM]: Augustus initial training results:
[05:31 AM]: Augustus optimized training results:
[05:31 AM]: Running Augustus gene prediction using trichoplax_adhaerens parameters
Traceback (most recent call last):
  File "/gpfs/ysm/project/dunn/jlm329/conda_envs/funannotate/lib/python2.7/site-packages/funannotate/aux_scripts/augustus_parallel.py", line 9, in <module>
    import funannotate.library as lib
ImportError: No module named funannotate.library
[05:31 AM]: Augustus prediction failed, check `logfiles/augustus-parallel.log`

OS/Install Information

Checking Environmental Variables...
$FUNANNOTATE_DB=/home/jlm329/project/trix/funannotate_db
$PASAHOME=/gpfs/ysm/project/dunn/jlm329/conda_envs/funannotate/opt/pasa-2.4.1
$TRINITY_HOME=/gpfs/ysm/project/dunn/jlm329/conda_envs/funannotate/opt/trinity-2.8.5
$EVM_HOME=/gpfs/ysm/project/dunn/jlm329/conda_envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/gpfs/ysm/project/dunn/jlm329/conda_envs/funannotate/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: 0.9.21
emapper.py: 2.0.1
ete3: 3.1.1
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2017-11-15
hisat2: 2.2.0
hmmscan: HMMER 3.3 (Nov 2019)
hmmsearch: HMMER 3.3 (Nov 2019)
java: 11.0.1-internal
kallisto: 0.46.2
mafft: v7.464 (2020/Apr/21)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.17-r941
proteinortho: 6.0.16
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.9
snap: 2006-07-28
stringtie: 2.1.2
tRNAscan-SE: 2.0.5 (October 2019)
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: Error occurred during initialization of VM
	ERROR: gmes_petap.pl not installed
	ERROR: signalp not installed

Issue Analytics

State:
Created 3 years ago
Comments:7 (2 by maintainers)

Top GitHub Comments

1reaction

jasminelmahcommented, May 22, 2020

The predict run worked! What seems to have happened is that I may have submitted the script from a messy environment. I started a new ssh session, loaded only miniconda and not the funannotate environment and submitted the job.

0reactions

hyphaltipcommented, Nov 18, 2022

if you are running on a slurm envirnoment you may want to use #!/usr/bin/bash -l to ensure a clean load of modules each time.

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