Kevin

It really, hard for me to install in my linux server, it ask for a lot of dependencies, help.

Unable to annotate genomes using funannotate ?

12

Hi, I'm trying to annotate the genomes, end up in python error. Need help. CMD- `funannotate predict -i Llips.R.fasta -s zebrafish --protein_evidence /home/sunn/data/softwares/gnom/test/spades/backup/Abininew/refgenome/tanaka.gff -o Llips --cpus 16 --force > Llips.log...

Apache Toree - PySpark error

2

Hi, I tried all the settings need to run PySpark Toree. Not able to figure out were it went wrong, suggestions! Name: org.apache.toree.interpreter.broker.BrokerException Message: Traceback (most recent call last): File...

Does the Braker.pl works with translation_table 2?

5

Hi , Can we run Braker.pl with translation_table = **2**, for annotating fish genomes. Suggestions please.

Unable to run BRAKER - Scalar::Util::Numeric error ?

6

Hi, I installed all the dependencies, and perl v5.16.3 is my default version in the centos 7 server. Suggestions please! ``` **cpan install Scalar::Util::Numeric** CPAN: Storable loaded ok (v2.45) Reading...

HI, `braker.pl --genome=Avscaffolds.spades.fasta --hints=prothint_augustus.gff --workingdir=brakergff_test --cores 10 ` BRAKER2 has run till this step -- **fixing AUGUSTUS genes with in frame stop codons...** **ERROR** in file /home/sun/data/softwares/BRAKER-2.1.6/scripts/**braker.pl at line 8334**...

Hi, I rerun the braker with ProtHint. **CMD** `braker.pl --genome=Aventri.contigs.velvet.cdhit.fa --prot_seq=orthodball.fasta --species=Sp_1 --cores 8 --workingdir=Avelvet1_test --PROTHINT_PATH=/home/sun/data/softwares/evaluation/ProtHint-2.6.0/bin` **It runs for some time, and this **error** pops up. If I run the...

Error: Unable to initialize main class phylonet.coalescent.CommandLine

2

**Describe the bug** Its a java error Error: Unable to initialize main class phylonet.coalescent.CommandLine Caused by: java.lang.NoClassDefFoundError: com/martiansoftware/jsap/StringParser **To Reproduce** `java -Xmx60g -jar astral.5.7.1.jar -i mlbest.trees -b mlboot.txt -o species_boot.trees...

Unable to configure sepp ?

3

Unable to install sepp, configuration error. Suggestions. python setup.py install --user running install running bdist_egg running egg_info writing sepp.egg-info/PKG-INFO writing dependency_links to sepp.egg-info/dependency_links.txt writing requirements to sepp.egg-info/requires.txt writing top-level names...

CAMSA - Can't we run in parallel mode

1

Hi, Is there any thread option to speed up the jobs ? I am trying to generate the meta-assembly for fish genomes, taking a longer time. Suggestions!