Braker3/GeneMark-ETP: file not found: complete.gtf, complete.id, complete_uniq.gtf

Hello,

Thank you for all the great tools coming from this team.

I gave Braker3 a shot, but am running into an error at the moment. I will report below how I installed Braker3, and how I used it in case it helps reproduce the error.

I would be grateful for any guidance you can provide, and am eager to get Braker3 working at some point in the near future, but fully understand that you are busy. I am mainly reporting this issue in case it helps your development.

First, here was the command used.

braker.pl --genome=${ASM} --UTR=on --stranded=+,- --bam=${FWD},${REV} --prot_seq=${PROTEINS} --workingdir=braker3 --threads=16

Second, here are the errors as reported.

This was reported to stdout/stderr.

# Fri Feb 24 08:59:35 2023: Creating directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3.
# Fri Feb 24 08:59:35 2023:Both protein and RNA-Seq libraries in input detected. BRAKER will be executed in ETP mode.
#*********
# Fri Feb 24 08:59:38 2023: Log information is stored in file /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/braker.log
#*********
# WARNING: Detected whitespace in fasta header of file /central/groups/carnegie_poc/jurban/software/braker2/protein/gfas1-and-hexacorallia-and-metazoan-proteins-orthoDB.fasta. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
#*********
ERROR in file /home/jurban/software/braker2/braker3/BRAKER/scripts/braker.pl at line 5486
Failed to execute: /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/perl /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/bin/gmetp.pl --cfg /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_config.yaml --workdir /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP --bam /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_data/ --cores 16 --softmask 1>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/GeneMark-ETP.stdout 2>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/GeneMark-ETP.stderr
Failed to execute: /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/perl /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/bin/gmetp.pl --cfg /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_config.yaml --workdir /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP --bam /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_data/ --cores 16 --softmask 1>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/GeneMark-ETP.stdout 2>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/GeneMark-ETP.stderr
The most common problem is an expired or not present file ~/.gm_key!

This is from braker.log


#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /home/jurban/software/braker2/braker3/BRAKER/scripts/braker.pl --genome=/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/longest.fa.masked --UTR=on --stranded=+,- --bam=/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/forward.bam,/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/reverse.bam --prot_seq=/central/groups/carnegie_poc/jurban/software/braker2/protein/gfas1-and-hexacorallia-and-metazoan-proteins-orthoDB.fasta --workingdir=braker3 --threads=16
# Fri Feb 24 08:59:35 2023: braker.pl version 3.0.0
# Fri Feb 24 08:59:35 2023: Creating directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3.
# Fri Feb 24 08:59:35 2023: Creating directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3.
# Fri Feb 24 08:59:35 2023:Both protein and RNA-Seq libraries in input detected. BRAKER will be executed in ETP mode.
#*********
# Fri Feb 24 08:59:35 2023: Configuring of BRAKER for using external tools...
# Fri Feb 24 08:59:35 2023: Trying to set $AUGUSTUS_CONFIG_PATH...
# Fri Feb 24 08:59:35 2023: Found environment variable $AUGUSTUS_CONFIG_PATH.
# Fri Feb 24 08:59:35 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/config/ as potential path for $AUGUSTUS_CONFIG_PATH.
# Fri Feb 24 08:59:35 2023: Success! Setting $AUGUSTUS_CONFIG_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/config/!
# Fri Feb 24 08:59:35 2023: Trying to set $AUGUSTUS_BIN_PATH...
# Fri Feb 24 08:59:35 2023: Found environment variable $AUGUSTUS_BIN_PATH.
# Fri Feb 24 08:59:35 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/ as potential path for $AUGUSTUS_BIN_PATH.
# Fri Feb 24 08:59:35 2023: Success! Setting $AUGUSTUS_BIN_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/!
# Fri Feb 24 08:59:35 2023: Trying to set $AUGUSTUS_SCRIPTS_PATH...
# Fri Feb 24 08:59:35 2023: Found environment variable $AUGUSTUS_SCRIPTS_PATH.
# Fri Feb 24 08:59:35 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/ as potential path for $AUGUSTUS_SCRIPTS_PATH.
# Fri Feb 24 08:59:35 2023: Success! Setting $AUGUSTUS_SCRIPTS_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/!
# Fri Feb 24 08:59:35 2023: Trying to set $PYTHON3_PATH...
# Fri Feb 24 08:59:35 2023: Did not find environment variable $PYTHON3_PATH.
# Fri Feb 24 08:59:35 2023: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH
# Fri Feb 24 08:59:35 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin as potential path for $PYTHON3_PATH.
# Fri Feb 24 08:59:35 2023: Success! Setting $PYTHON3_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin!
# Fri Feb 24 08:59:35 2023: Trying to set $JAVA_PATH...
# Fri Feb 24 08:59:35 2023: Did not find environment variable $JAVA_PATH.
# Fri Feb 24 08:59:35 2023: Trying to guess JAVA_PATH from location of java executable that is available in your $PATH
# Fri Feb 24 08:59:35 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin as potential path for $JAVA_PATH.
# Fri Feb 24 08:59:35 2023: Success! Setting $JAVA_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin!
# Fri Feb 24 08:59:36 2023: Trying to set $GUSHR_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $GUSHR_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess GUSHR_PATH from location of gushr.py executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin as potential path for $GUSHR_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $GUSHR_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin!
# Fri Feb 24 08:59:36 2023: Trying to set $GENEMARK_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $GENEMARK_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess GENEMARK_PATH from location of gmetp.pl executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/bin as potential path for $GENEMARK_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $GENEMARK_PATH to /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/bin!
# Fri Feb 24 08:59:36 2023: Trying to set $BAMTOOLS_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $BAMTOOLS_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess BAMTOOLS_PATH from location of bamtools executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin as potential path for $BAMTOOLS_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $BAMTOOLS_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin!
# Fri Feb 24 08:59:36 2023: Trying to set $SAMTOOLS_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $SAMTOOLS_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess SAMTOOLS_PATH from location of samtools executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/tools as potential path for $SAMTOOLS_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $SAMTOOLS_PATH to /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/tools!
# Fri Feb 24 08:59:36 2023: Trying to set $DIAMOND_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $DIAMOND_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess DIAMOND_PATH from location of diamond executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/tools as potential path for $DIAMOND_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $DIAMOND_PATH to /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/tools!
# Fri Feb 24 08:59:36 2023: Trying to set $PROTHINT_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $PROTHINT_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess PROTHINT_PATH from location of prothint.py executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/braker2/deps/prothint/ProtHint-2.6.0/bin as potential path for $PROTHINT_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $PROTHINT_PATH to /central/groups/carnegie_poc/jurban/software/braker2/deps/prothint/ProtHint-2.6.0/bin!
# Fri Feb 24 08:59:36 2023: Trying to set $TSEBRA_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $TSEBRA_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess TSEBRA_PATH from location of tsebra.py executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin as potential path for $TSEBRA_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $TSEBRA_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin!
# Fri Feb 24 08:59:36 2023: Trying to set $CDBTOOLS_PATH...
# Fri Feb 24 08:59:36 2023: Did not find environment variable $CDBTOOLS_PATH.
# Fri Feb 24 08:59:36 2023: Trying to guess CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH
# Fri Feb 24 08:59:36 2023: Checking /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin as potential path for $CDBTOOLS_PATH.
# Fri Feb 24 08:59:36 2023: Success! Setting $CDBTOOLS_PATH to /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin!
#*********
# IMPORTANT INFORMATION: no species for identifying the AUGUSTUS  parameter set that will arise from this BRAKER run was set. BRAKER will create an AUGUSTUS parameter set with name Sp_1. This parameter set can be used for future BRAKER/AUGUSTUS prediction runs for the same species. It is usually not necessary to retrain AUGUSTUS with novel extrinsic data if a high quality parameter set already exists.
#*********
#**********************************************************************************
#                               CREATING DIRECTORY STRUCTURE                       
#**********************************************************************************
# Fri Feb 24 08:59:38 2023: creating file that contains citations for this BRAKER run at /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/what-to-cite.txt...
# Fri Feb 24 08:59:38 2023: create working directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP.
mkdir /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP
# Fri Feb 24 08:59:38 2023: create working directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/species
mkdir /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/species
# Fri Feb 24 08:59:38 2023: create working directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors
mkdir /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors
# Fri Feb 24 08:59:38 2023: changing into working directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3
cd /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3
# Fri Feb 24 08:59:38 2023: getting GC content of the genome
/central/groups/carnegie_poc/jurban/software/braker2/braker3/BRAKER/scripts/get_gc_content.py --sequences /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/longest.fa.masked --print_sequence_length 1> /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/gc_content.out 2> /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/gc_content.stderr
# Fri Feb 24 08:59:40 2023: Creating parameter template files for AUGUSTUS with new_species.pl
# Fri Feb 24 08:59:40 2023: new_species.pl will create parameter files for species Sp_1 in /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/config//species/Sp_1
/central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/perl /central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/new_species.pl --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/config/ 1> /dev/null 2>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/new_species.stderr
# Fri Feb 24 08:59:40 2023: check_fasta_headers(): Checking fasta headers of file /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/longest.fa.masked
# Fri Feb 24 08:59:40 2023: check_fasta_headers(): Checking fasta headers of file /central/groups/carnegie_poc/jurban/software/braker2/protein/gfas1-and-hexacorallia-and-metazoan-proteins-orthoDB.fasta
# Fri Feb 24 08:59:40 2023: Assuming that this is not a DNA fasta file because other characters than A, T, G, C, N, a, t, g, c, n were contained. If this is supposed to be a DNA fasta file, check the content of your file! If this is supposed to be a protein fasta file, please ignore this message!
#*********
# WARNING: Detected whitespace in fasta header of file /central/groups/carnegie_poc/jurban/software/braker2/protein/gfas1-and-hexacorallia-and-metazoan-proteins-orthoDB.fasta. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
#*********
# Fri Feb 24 08:59:44 2023: Assuming that this is not a protein fasta file because other characters than AaRrNnDdCcEeQqGgHhIiLlKkMmFfPpSsTtWwYyVvBbZzJjOoUuXx were contained. If this is supposed to be DNA fasta file, please ignore this message.
#**********************************************************************************
#                               PROCESSING HINTS                                   
#**********************************************************************************
#**********************************************************************************
#                              RUNNING GENEMARK-EX                                 
#**********************************************************************************
# Fri Feb 24 09:00:15 2023: Preparing genemark_evidence file hints from manual hints...
# Fri Feb 24 09:00:15 2023: Running GeneMark-ETP
# Fri Feb 24 09:00:15 2023: changing into GeneMark-ETP directory /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP
cd /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP
# Fri Feb 24 09:00:16 2023: sorting RNA-Seq BAM files
samtools sort /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/forward.bam -o /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_data/forward.bam 1> /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/samtools.sort.forward.stdout 2> /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/samtools.sort.forward.stderr
samtools sort /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/data/toy/reverse.bam -o /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_data/reverse.bam 1> /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/samtools.sort.reverse.stdout 2> /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/samtools.sort.reverse.stderr
# Fri Feb 24 09:00:32 2023: Running gmetp.pl
/central/groups/carnegie_poc/jurban/software/conda/anaconda3/envs/braker3-deps2/bin/perl /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/bin/gmetp.pl --cfg /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_config.yaml --workdir /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP --bam /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/etp_data/ --cores 16 --softmask 1>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/GeneMark-ETP.stdout 2>/central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/errors/GeneMark-ETP.stderr


------------------------------

>> **This is from GeneMark-ETP.stderr.**

FASTA index file /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/data/genome.softmasked.fasta.fai created. error, file not found: option --f1 complete.gtf error on open file complete.id: No such file or directory mv: cannot stat ‘complete_uniq.gtf’: No such file or directory error on open file /central/groups/carnegie_poc/jurban/data/coral/scratch/toyanno/braker3/braker3/GeneMark-ETP/rnaseq/hints/proteins.fa/complete.gtf: No such file or directory error on create_regions.pl at /central/groups/carnegie_poc/jurban/software/braker2/braker3/deps/genemark-etp/GeneMark-ETP/bin/gmetp.pl line 2162.


------------------------------

------------------------------

**Third, here is how I installed it.**

------------------------------

> First, I installed dependencies with Mamba (conda) using a YML file.

mamba env create -f braker3-deps.yml

I will copy/paste the `braker3-deps.yml` at the very bottom.

> Second, I installed GeneMark-ETP via git clone.

git clone https://github.com/gatech-genemark/GeneMark-ETP.git


>Third, I cloned BRAKER and checked out the braker3 branch.

git clone https://github.com/Gaius-Augustus/BRAKER.git cd BRAKER git checkout braker3


> Fourth, the run evironment is set by:

conda activate braker3-deps2 export PATH=${BRAKER3}:${GENEMARK_ETP_BIN}:${GENEMARK_ETP_TOOLS}:${PROTHINT2}:${PATH}


---------------------------------------
---------------------------------------
---------------------------------------
**YML File**

name: braker3-deps2 channels:

eumetsat
conda-forge
bioconda
defaults dependencies:
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=2_gnu
alsa-lib=1.2.7.2=h166bdaf_0
augustus=3.4.0=pl5262h5a9fe7b_2
bamtools=2.5.1=hd03093a_10
bedtools=2.30.0=h468198e_3
biopython=1.81=py310h1fa729e_0
blast=2.13.0=hf3cf87c_0
boost-cpp=1.74.0=h75c5d50_8
braker2=2.1.6=hdfd78af_5
bzip2=1.0.8=h7f98852_4
c-ares=1.18.1=h7f98852_0
ca-certificates=2022.12.7=ha878542_0
cairo=1.16.0=ha61ee94_1014
cdbtools=0.99=hd03093a_7
curl=7.87.0=h6312ad2_0
diamond=2.1.3=hb97b32f_0
entrez-direct=16.2=he881be0_1
exonerate=2.4.0=h09da616_5
expat=2.5.0=h27087fc_0
font-ttf-dejavu-sans-mono=2.37=hab24e00_0
font-ttf-inconsolata=3.000=h77eed37_0
font-ttf-source-code-pro=2.038=h77eed37_0
font-ttf-ubuntu=0.83=hab24e00_0
fontconfig=2.14.2=h14ed4e7_0
fonts-conda-ecosystem=1=0
fonts-conda-forge=1=0
freetype=2.12.1=hca18f0e_1
gawk=5.1.0=h7f98852_0
gemoma=1.6.4=hdfd78af_1
genomethreader=1.7.1=h87f3376_4
gettext=0.21.1=h27087fc_0
gffread=0.12.7=hd03093a_1
giflib=5.2.1=h36c2ea0_2
glib=2.74.1=h6239696_1
glib-tools=2.74.1=h6239696_1
gmp=6.2.1=h58526e2_0
graphite2=1.3.13=h58526e2_1001
gsl=2.6=he838d99_2
harfbuzz=5.3.0=h418a68e_0
hisat2=2.2.1=h87f3376_4
htslib=1.12=h9093b5e_1
icu=70.1=h27087fc_0
jbig=2.1=h7f98852_2003
jpeg=9e=h0b41bf4_3
keyutils=1.6.1=h166bdaf_0
krb5=1.20.1=hf9c8cef_0
lcms2=2.12=hddcbb42_0
ld_impl_linux-64=2.40=h41732ed_0
lerc=2.2.1=h9c3ff4c_0
libblas=3.9.0=16_linux64_openblas
libcblas=3.9.0=16_linux64_openblas
libcups=2.3.3=h36d4200_3
libcurl=7.87.0=h6312ad2_0
libdeflate=1.7=h7f98852_5
libedit=3.1.20191231=he28a2e2_2
libev=4.33=h516909a_1
libffi=3.4.2=h7f98852_5
libgcc-ng=12.2.0=h65d4601_19
libgfortran-ng=12.2.0=h69a702a_19
libgfortran5=12.2.0=h337968e_19
libglib=2.74.1=h606061b_1
libgomp=12.2.0=h65d4601_19
libhwloc=2.8.0=h32351e8_1
libiconv=1.17=h166bdaf_0
libidn2=2.3.4=h166bdaf_0
liblapack=3.9.0=16_linux64_openblas
libnghttp2=1.51.0=hdcd2b5c_0
libnsl=2.0.0=h7f98852_0
libopenblas=0.3.21=pthreads_h78a6416_3
libpng=1.6.39=h753d276_0
libssh2=1.10.0=haa6b8db_3
libstdcxx-ng=12.2.0=h46fd767_19
libtiff=4.3.0=hf544144_1
libunistring=0.9.10=h7f98852_0
libuuid=2.32.1=h7f98852_1000
libwebp-base=1.2.4=h166bdaf_0
libxcb=1.13=h7f98852_1004
libxml2=2.9.14=h22db469_4
libzlib=1.2.13=h166bdaf_4
lp_solve=5.5.2.5=h14c3975_1001
makehub=1.0.5=1
metis=5.1.0=h58526e2_1006
mmseqs2=13.45111=h95f258a_1
mpfr=4.1.0=h9202a9a_1
mysql-connector-c=6.1.11=h6eb9d5d_1007
ncbi-vdb=3.0.2=h87f3376_0
ncurses=6.2=h58526e2_4
numpy=1.24.2=py310h8deb116_0
openjdk=8.0.332=h166bdaf_0
openssl=1.1.1t=h0b41bf4_0
ossuuid=1.6.2=hf484d3e_1000
pcre=8.45=h9c3ff4c_0
pcre2=10.40=hc3806b6_0
perl=5.26.2=h36c2ea0_1008
perl-apache-test=1.40=pl526_1
perl-app-cpanminus=1.7044=pl526_1
perl-archive-tar=2.32=pl526_0
perl-base=2.23=pl526_1
perl-business-isbn=3.004=pl526_0
perl-business-isbn-data=20140910.003=pl526_0
perl-carp=1.38=pl526_3
perl-class-data-inheritable=0.08=pl526_1
perl-class-load=0.25=pl526_0
perl-class-load-xs=0.10=pl526h6bb024c_2
perl-class-method-modifiers=2.12=pl526_0
perl-clone-choose=0.010=pl526_0
perl-common-sense=3.74=pl526_2
perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
perl-compress-raw-zlib=2.087=pl526hc9558a2_0
perl-constant=1.33=pl526_1
perl-cpan-meta=2.150010=pl526_0
perl-cpan-meta-requirements=2.140=pl526_0
perl-cpan-meta-yaml=0.018=pl526_0
perl-data-dumper=2.173=pl526_0
perl-data-optlist=0.110=pl526_2
perl-dbi=1.642=pl526_0
perl-devel-globaldestruction=0.14=pl526_0
perl-devel-overloadinfo=0.005=pl526_0
perl-devel-stacktrace=2.04=pl526_0
perl-dist-checkconflicts=0.11=pl526_2
perl-encode=2.88=pl526_1
perl-eval-closure=0.14=pl526h6bb024c_4
perl-exception-class=1.44=pl526_0
perl-exporter=5.72=pl526_1
perl-exporter-tiny=1.002001=pl526_0
perl-extutils-cbuilder=0.280230=pl526_1
perl-extutils-makemaker=7.36=pl526_1
perl-extutils-manifest=1.72=pl526_0
perl-extutils-parsexs=3.35=pl526_0
perl-file-homedir=1.004=pl526_2
perl-file-path=2.16=pl526_0
perl-file-spec=3.48_01=pl526_1
perl-file-temp=0.2304=pl526_2
perl-file-which=1.23=pl526_0
perl-getopt-long=2.50=pl526_1
perl-hash-merge=0.300=pl526_0
perl-inline=0.80=pl526_2
perl-io-compress=2.087=pl526he1b5a44_0
perl-io-zlib=1.10=pl526_2
perl-ipc-cmd=1.02=pl526_0
perl-json=4.02=pl526_0
perl-json-pp=4.04=pl526_0
perl-json-xs=2.34=pl526h6bb024c_3
perl-list-moreutils=0.428=pl526_1
perl-list-moreutils-xs=0.428=pl526_0
perl-list-util=1.38=pl526_1
perl-locale-maketext-simple=0.21=pl526_2
perl-logger-simple=2.0=pl526_0
perl-math-utils=1.13=pl526_0
perl-mce=1.837=pl526_0
perl-mime-base64=3.15=pl526_1
perl-module-build=0.4224=pl526_3
perl-module-corelist=5.20190524=pl526_0
perl-module-implementation=0.09=pl526_2
perl-module-load=0.32=pl526_1
perl-module-load-conditional=0.68=pl526_2
perl-module-metadata=1.000036=pl526_0
perl-module-runtime=0.016=pl526_1
perl-module-runtime-conflicts=0.003=pl526_0
perl-moo=2.003004=pl526_0
perl-moose=2.2011=pl526hf484d3e_1
perl-mro-compat=0.13=pl526_0
perl-object-insideout=4.05=pl526_0
perl-package-deprecationmanager=0.17=pl526_0
perl-package-stash=0.38=pl526hf484d3e_1
perl-package-stash-xs=0.28=pl526hf484d3e_1
perl-parallel-forkmanager=2.02=pl526_0
perl-params-check=0.38=pl526_1
perl-params-util=1.07=pl526h6bb024c_4
perl-parent=0.236=pl526_1
perl-pathtools=3.75=pl526h14c3975_1
perl-perl-ostype=1.010=pl526_1
perl-posix=1.38_03=pl526_1
perl-role-tiny=2.000008=pl526_0
perl-scalar-list-utils=1.52=pl526h516909a_0
perl-scalar-util-numeric=0.40=pl526_1
perl-socket=2.027=pl526_1
perl-storable=3.15=pl526h14c3975_0
perl-sub-exporter=0.987=pl526_2
perl-sub-exporter-progressive=0.001013=pl526_0
perl-sub-identify=0.14=pl526h14c3975_0
perl-sub-install=0.928=pl526_2
perl-sub-name=0.21=pl526_1
perl-sub-quote=2.006003=pl526_1
perl-test-harness=3.42=pl526_0
perl-test-pod=1.52=pl526_0
perl-text-abbrev=1.02=pl526_0
perl-text-parsewords=3.30=pl526_0
perl-time-hires=1.9760=pl526h14c3975_1
perl-try-tiny=0.30=pl526_1
perl-types-serialiser=1.0=pl526_2
perl-uri=1.76=pl526_0
perl-version=0.9924=pl526_0
perl-xml-libxml=2.0132=pl526h7ec2d77_1
perl-xml-namespacesupport=1.12=pl526_0
perl-xml-sax=1.02=pl526_0
perl-xml-sax-base=1.09=pl526_0
perl-xsloader=0.24=pl526_0
perl-yaml=1.29=pl526_0
perl-yaml-xs=0.74=pl526h14c3975_0
pip=23.0.1=pyhd8ed1ab_0
pixman=0.40.0=h36c2ea0_0
pthread-stubs=0.4=h36c2ea0_1001
python=3.10.2=h62f1059_0_cpython
python_abi=3.10=3_cp310
readline=8.1=h46c0cb4_0
samtools=1.12=h9aed4be_1
setuptools=67.4.0=pyhd8ed1ab_0
spaln=2.4.7=pl5262h9a82719_0
sqlite=3.37.0=h9cd32fc_0
sra-tools=3.0.3=h87f3376_0
stringtie=2.2.1=h3198e80_0
suitesparse=5.10.1=h9e50725_1
tar=1.34=hb2e2bae_1
tbb=2021.7.0=h924138e_1
tk=8.6.12=h27826a3_0
tzdata=2022g=h191b570_0
ucsc-bedtobigbed=377=ha8a8165_3
ucsc-fatotwobit=377=ha8a8165_5
ucsc-genepredcheck=377=ha8a8165_3
ucsc-genepredtobed=377=ha8a8165_5
ucsc-genepredtobiggenepred=377=ha8a8165_3
ucsc-gtftogenepred=377=ha8a8165_5
ucsc-hggcpercent=377=ha8a8165_3
ucsc-ixixx=377=ha8a8165_3
ucsc-twobitinfo=377=ha8a8165_3
ucsc-wigtobigwig=377=ha8a8165_3
wget=1.20.3=ha56f1ee_1
wheel=0.38.4=pyhd8ed1ab_0
xorg-fixesproto=5.0=h7f98852_1002
xorg-inputproto=2.3.2=h7f98852_1002
xorg-kbproto=1.0.7=h7f98852_1002
xorg-libice=1.0.10=h7f98852_0
xorg-libsm=1.2.3=hd9c2040_1000
xorg-libx11=1.7.2=h7f98852_0
xorg-libxau=1.0.9=h7f98852_0
xorg-libxdmcp=1.1.3=h7f98852_0
xorg-libxext=1.3.4=h0b41bf4_2
xorg-libxfixes=5.0.3=h7f98852_1004
xorg-libxi=1.7.10=h7f98852_0
xorg-libxrender=0.9.10=h7f98852_1003
xorg-libxtst=1.2.3=h7f98852_1002
xorg-recordproto=1.14.2=h7f98852_1002
xorg-renderproto=0.11.1=h7f98852_1002
xorg-xextproto=7.3.0=h0b41bf4_1003
xorg-xproto=7.0.31=h7f98852_1007
xz=5.2.6=h166bdaf_0
zlib=1.2.13=h166bdaf_4
zstd=1.5.2=h3eb15da_6

NOTE: This conda environment was originally created on a separate system this way:
mamba create -n braker3-deps2 -c bioconda braker2 hisat2 stringtie bedtools sra-tools gffread
conda activate braker3-deps2
mamba install -c eumetsat perl-yaml-xs
mamba install -c conda-forge openjdk=8
And YML file obtained by:
conda env export > braker3-deps2.yml

Gaius-Augustus / BRAKER

Braker3/GeneMark-ETP: file not found: complete.gtf, complete.id, complete_uniq.gtf #577