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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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--UTR=on not working due to java error #766

Closed LliliansCalvo closed 4 months ago

LliliansCalvo commented 4 months ago

Hi,

The command bellow works fine without the --UTR=on but as soon as I add it I get the error bellow. However java is installed on my system as you can see. How could I solve this?

# Execute the Braker command for each sample
singularity exec ${SINGULARITY_IMAGE} braker.pl --species=Cfellah --useexisting --gff3 --UTR=on  --genome=${GENOME_FILE} --prot_seq=/scratch/lcalvogo/Braker/proteins.fasta --softmasking --threads 8 --gm_max_intergenic 10000 \
--rnaseq_sets_ids="SRR24634940,SRR24634941,SRR24634942,SRR24634946,SRR24634936,SRR24634938" \
--rnaseq_sets_dirs="$(find ${RNA_SEQ_DIR} -name "SRR24634940_1.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634940_2.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634941_1.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634941_2.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634942_1.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634942_2.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634946_1.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634946_2.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634936_1.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634936_2.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634938_1.fastq"),$(find ${RNA_SEQ_DIR} -name "SRR24634938_2.fastq")"

#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /opt/BRAKER/scripts/braker.pl --species=Cfellah --useexisting --gff3 --UTR=on --genome=/work/FAC/FBM/CIG/rbenton/neuroflies/Gilly/genome/mod_GCA_030586385.1_ASM3058638v1_genomic.fa --prot_seq=/scratch/lcalvogo/Braker/proteins.fasta --softmasking --threads 8 --gm_max_intergenic 10000 --rnaseq_sets_ids=SRR24634940,SRR24634941,SRR24634942,SRR24634946,SRR24634936,SRR24634938 --rnaseq_sets_dirs=/scratch/lcalvogo/Tomas_Kay_data/SRR24634940_1.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634940_2.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634941_1.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634941_2.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634942_1.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634942_2.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634946_1.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634946_2.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634936_1.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634936_2.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634938_1.fastq,/scratch/lcalvogo/Tomas_Kay_data/SRR24634938_2.fastq
# Mon Feb 19 13:08:17 2024: braker.pl version 3.0.6
# Mon Feb 19 13:08:17 2024:Both protein and RNA-Seq data in input detected. BRAKER will be executed in ETP mode (BRAKER3).
#*********
# Mon Feb 19 13:08:17 2024: Configuring of BRAKER for using external tools...
# Mon Feb 19 13:08:17 2024: Searching for local files of RNA-Seq sets in /scratch/lcalvogo/Tomas_Kay_data/SRR24634940_1.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634940_2.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634941_1.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634941_2.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634942_1.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634942_2.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634946_1.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634946_2.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634936_1.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634936_2.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634938_1.fastq, /scratch/lcalvogo/Tomas_Kay_data/SRR24634938_2.fastq ...
# Mon Feb 19 13:08:17 2024: Couldn't find local RNA-Seq library for SRR24634940, will try to download it from SRA later.
# Mon Feb 19 13:08:17 2024: Couldn't find local RNA-Seq library for SRR24634941, will try to download it from SRA later.
# Mon Feb 19 13:08:17 2024: Couldn't find local RNA-Seq library for SRR24634942, will try to download it from SRA later.
# Mon Feb 19 13:08:17 2024: Couldn't find local RNA-Seq library for SRR24634946, will try to download it from SRA later.
# Mon Feb 19 13:08:17 2024: Couldn't find local RNA-Seq library for SRR24634936, will try to download it from SRA later.
# Mon Feb 19 13:08:17 2024: Couldn't find local RNA-Seq library for SRR24634938, will try to download it from SRA later.
# Mon Feb 19 13:08:17 2024: Trying to set $AUGUSTUS_CONFIG_PATH...
# Mon Feb 19 13:08:17 2024: Found environment variable $AUGUSTUS_CONFIG_PATH.
# Mon Feb 19 13:08:17 2024: Checking /usr/share/augustus/config/ as potential path for $AUGUSTUS_CONFIG_PATH.
# Mon Feb 19 13:08:17 2024: Success! Setting $AUGUSTUS_CONFIG_PATH to /usr/share/augustus/config/!
# Mon Feb 19 13:08:17 2024: WARNING: in file /opt/BRAKER/scripts/braker.pl at line 1894
AUGUSTUS_CONFIG_PATH/species (in this case /usr/share/augustus/config//species) is not writeable. BRAKER will try to copy the AUGUSTUS config directory to a writeable location.
# Mon Feb 19 13:08:17 2024: Trying to set $AUGUSTUS_BIN_PATH...
# Mon Feb 19 13:08:17 2024: Found environment variable $AUGUSTUS_BIN_PATH.
# Mon Feb 19 13:08:17 2024: Checking /usr/bin/ as potential path for $AUGUSTUS_BIN_PATH.
# Mon Feb 19 13:08:17 2024: Success! Setting $AUGUSTUS_BIN_PATH to /usr/bin/!
# Mon Feb 19 13:08:17 2024: Trying to set $AUGUSTUS_SCRIPTS_PATH...
# Mon Feb 19 13:08:17 2024: Found environment variable $AUGUSTUS_SCRIPTS_PATH.
# Mon Feb 19 13:08:17 2024: Checking /usr/share/augustus/scripts/ as potential path for $AUGUSTUS_SCRIPTS_PATH.
# Mon Feb 19 13:08:17 2024: Success! Setting $AUGUSTUS_SCRIPTS_PATH to /usr/share/augustus/scripts/!
# Mon Feb 19 13:08:17 2024: WARNING: BRAKER will copy the
 AUGUSTUS_CONFIG folder into your home directory!
# Mon Feb 19 13:08:17 2024: WARNING: $AUGUSTUS_CONFIG_PATH/species (in this case /usr/share/augustus/config//species ) is not writeable.
*** IMPORTANT: Resetting $AUGUSTUS_CONFIG_PATH=/users/lcalvogo/.augustus because BRAKER requires a writable location!
# Mon Feb 19 13:08:17 2024: Trying to set $PYTHON3_PATH...
# Mon Feb 19 13:08:17 2024: Did not find environment variable $PYTHON3_PATH.
# Mon Feb 19 13:08:17 2024: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH
# Mon Feb 19 13:08:17 2024: Checking /opt/conda/bin as potential path for $PYTHON3_PATH.
# Mon Feb 19 13:08:17 2024: Success! Setting $PYTHON3_PATH to /opt/conda/bin!
# Mon Feb 19 13:08:17 2024: Trying to set $JAVA_PATH...
# Mon Feb 19 13:08:17 2024: Did not find environment variable $JAVA_PATH.
# Mon Feb 19 13:08:17 2024: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 1795
$JAVA_PATH not set!
There are 3 alternative ways to set JAVA_PATH for
braker.pl:
   a) provide command-line argument --JAVA_PATH=/your/path
   b) use an existing environment variable $JAVA_PATH
      for setting the environment variable, run
           export JAVA_PATH=/your/path
      in your shell. You may append this to your .bashrc or 
      .profile file in order to make the variable available to
      all your bash sessions.
   c) braker.pl can try guessing the location of 
      JAVA_PATH from the location of java
      executable if it is available in your $PATH variable.
      If you try to rely on this option, you can check by
      typing
           which java
      in your shell, whether the executable is in your $PATH
# Mon Feb 19 13:08:17 2024:Both protein and RNA-Seq data in input detected. BRAKER will be executed in ETP mode (BRAKER3).
#*********
java -version
openjdk version "1.8.0_372"
OpenJDK Runtime Environment (build 1.8.0_372-b07)
OpenJDK 64-Bit Server VM (build 25.372-b07, mixed mode)
Bank-tidy commented 4 months ago

I encountered the same problem.

KatharinaHoff commented 4 months ago

Please do not use the UTR feature. We have no resources to debug it.