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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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Illegal division by zero at galba.pl line 4856. #1

Closed JuFengWang closed 1 year ago

JuFengWang commented 1 year ago

Hi I tried to run galba.pl to annotate genome with command below: galba.pl --threads 24 --species=test --genome=/soft/galba/example/genome.fa --prot_seq=/soft/galba/example/proteins.fa But I get the error:

Can't exec "getconf": No such file or directory at /soft/galba/scripts/galba.pl line 2688.
Use of uninitialized value $cpus_available in numeric lt (<) at /soft/galba/scripts/galba.pl line 2690.
Use of uninitialized value $cpus_available in concatenation (.) or string at /soft/galba/scripts/galba.pl line 2691.
Use of uninitialized value $cpus_available in concatenation (.) or string at /soft/galba/scripts/galba.pl line 2691.
# Mon Nov 28 18:07:21 2022: Log information is stored in file /Tmusculi/annotation/galba/GALBA/GALBA.log
[WARNING] unrecognized option
[M::mp_idx_restore@0.091*1.00] loaded the index
[M::mp_idx_print_stat] 170802 distinct k-mers; mean occ of infrequent k-mers: 1.72; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::0.178*6.34] mapped 259 sequences
[M::main] Version: 0.5-r179
[M::main] CMD: /miniconda3/envs/galba/bin/miniprot -ut24 --gtf /Tmusculi/annotation/galba/GALBA/genome.mpi /soft/galba/example/proteins.fa
[M::main] Real time: 0.189 sec; CPU: 1.137 sec; Peak RSS: 0.139 GB
Argument "-" isn't numeric in numeric lt (<) at /soft/galba/scripts/aln2hints.pl line 226, <ALN> line 1.
Argument "+" isn't numeric in numeric lt (<) at /soft/galba/scripts/aln2hints.pl line 226, <ALN> line 2.

.....

Argument "-" isn't numeric in numeric lt (<) at /soft/galba/scripts/aln2hints.pl line 226, <ALN> line 261.
Argument "-" isn't numeric in numeric lt (<) at /soft/galba/scripts/aln2hints.pl line 226, <ALN> line 262.
Illegal division by zero at /soft/galba/scripts/galba.pl line 4856.

While the scripts work well with parameter -prg=gth.

GALBA.log

Thank you for any help!

KatharinaHoff commented 1 year ago

galba.pl uses getconf to see how many threads your hardware provides. You can install getconf on Ubuntu with e.g.

apt-get install libc-bin

The Docker and Singularity container both have getconf. I will add the requirement to the README.md