Augustus

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when I try to make, it happened ''' cd auxprogs/filterBam/src make g++ -std=c++0x filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz /usr/bin/ld: 找不到 -lbamtools collect2:...

zhouyflab

Thanks for this wonderful developed software for genome annotation My question is can i use this protocol to annotate contig assembly without scaffolds? Thanks

naahraissa

Cannot find multiple dependencies

9

Hello, Unfortunately I am getting errors during the installation when I type "make". > /usr/bin/ld: cannot find -llpsolve55 > /usr/bin/ld: cannot find -lcolamd > /usr/bin/ld: cannot find -lmysqlclient > /usr/bin/ld:...

FabianDK

When trying to build `augustus` with boost 1.76, I obtain the following error: ``` In file included from /usr/local/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/local/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/local/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/local/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/local/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:29, from...

Moisan

bam2hints distributed with AUGUSTUS crashes with some BAM-files as input (Error: Segmentation fault (core dumped)). However, bam2hints distributed with VARUS runs smoothly on them. A minimal example with bam2hints call...

lazlostrange

Patch 1

1

bam2wig cant make i copy bam2wig binary from https://raw.githubusercontent.com/MikeAxtell/bam2wig/master/bam2wig

atongsa

Augustus PPX mode: augustInvalid block no. error

2

Hi there, I've made a small prototype Nextflow pipeline to run Augustus in PPX mode with custom protein profiles, via Docker or Singularity: https://github.com/photocyte/luciferase-PPX-predictor-nf ( Augustus Docker image from `quay.io/biocontainers/augustus:3.4.0--pl5321hd8b735c_3`...

photocyte

As part of a project to evaluate the performance of various annotation pipelines, we have run Augustus in comparative mode to jointly annotate three butterfly species, and using MAFs generated...

adamfreedman

Hi, I want to generate training gene structures from assembled NovaSeq sequence data and PacBio (Sequel II) genome sequences. I followed the procedures in the “augustus.wrp.pdf” and stuck at: :$...

menoxx

There appears to be an issue with the script gff2gbSmallDNA.pl. When applying gff2gbSmallDNA.pl to GeneMarkS-T predictions made on transcripts assembled by StringTie2, fewer transcripts are output than are input. This...

lazlostrange