Hello, I'm trying to run funannotate2 with singularity. These are my commands so far:
Singularity command
fun2="singularity exec
--bind /scr1/users/dirksa/db/fun2db:/funannotate2_db
--bind "$fcs_dir":"$fcs_dir"
--bind "$outdir":"$outdir"
--env FUNANNOTATE2_DB=/funannotate2_db
/home/dirksa/software/funannotate2/funannotate2_latest.sif"
$fun2 funannotate2 -h
Clean the genome
$fun2 funannotate2 clean -f "$genome" -o "$outdir/cleaned_genome.fasta" -m 1000 -r scaffold_
Train ab initio gene predictors
This step is optional. The output can be reused for other genomes.
$fun2 funannotate2 train -f "$outdir/cleaned_genome.fasta" -s "Candida tropicalis" -o "$outdir" --strain "$run" --cpus "$threads"
I'm encountering an error with the train step.
[Sep 17 10:16 AM] CMD ERROR: trainGlimmerHMM /scr1/users/dirksa/candida/seqs/funannotate2/ONCO0025/train_misc/glimmerhmm/glimmer.fasta /scr1/users/dirksa/candida/seqs/funannotate2/ONCO0025/train_misc/glimmerhmm/glimmer.exons -d train
[Sep 17 10:16 AM] Can't locate orf.pm: /opt/glimmerhmm/bin/../share/glimmerhmm/train/orf.pm: Permission denied at /opt/glimmerhmm/bin/trainGlimmerHMM line 16.
BEGIN failed--compilation aborted at /opt/glimmerhmm/bin/trainGlimmerHMM line 16.
I think there is a permissions issue with the sif
[𓆑 ONCO0025]$ singularity exec ~/software/funannotate2/funannotate2_latest.sif \
ls -l /opt/glimmerhmm/share/glimmerhmm/train/orf.pm
-rw-r-----. 1 root root 3127 Jun 21 12:52 /opt/glimmerhmm/share/glimmerhmm/train/orf.pm
Do you know how to fix this? Thanks!
Hello, I'm trying to run funannotate2 with singularity. These are my commands so far:
Singularity command
fun2="singularity exec
--bind /scr1/users/dirksa/db/fun2db:/funannotate2_db
--bind "$fcs_dir":"$fcs_dir"
--bind "$outdir":"$outdir"
--env FUNANNOTATE2_DB=/funannotate2_db
/home/dirksa/software/funannotate2/funannotate2_latest.sif"
$fun2 funannotate2 -h
Clean the genome
$fun2 funannotate2 clean -f "$genome" -o "$outdir/cleaned_genome.fasta" -m 1000 -r scaffold_
Train ab initio gene predictors
This step is optional. The output can be reused for other genomes.
$fun2 funannotate2 train -f "$outdir/cleaned_genome.fasta" -s "Candida tropicalis" -o "$outdir" --strain "$run" --cpus "$threads"
I'm encountering an error with the train step.
[Sep 17 10:16 AM] CMD ERROR: trainGlimmerHMM /scr1/users/dirksa/candida/seqs/funannotate2/ONCO0025/train_misc/glimmerhmm/glimmer.fasta /scr1/users/dirksa/candida/seqs/funannotate2/ONCO0025/train_misc/glimmerhmm/glimmer.exons -d train
[Sep 17 10:16 AM] Can't locate orf.pm: /opt/glimmerhmm/bin/../share/glimmerhmm/train/orf.pm: Permission denied at /opt/glimmerhmm/bin/trainGlimmerHMM line 16.
BEGIN failed--compilation aborted at /opt/glimmerhmm/bin/trainGlimmerHMM line 16.
I think there is a permissions issue with the sif
[𓆑 ONCO0025]$ singularity exec ~/software/funannotate2/funannotate2_latest.sif \
ls -l /opt/glimmerhmm/share/glimmerhmm/train/orf.pm
-rw-r-----. 1 root root 3127 Jun 21 12:52 /opt/glimmerhmm/share/glimmerhmm/train/orf.pm
Do you know how to fix this? Thanks!