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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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docker error: bamtools not installed. #732

Closed leon945945 closed 7 months ago

leon945945 commented 8 months ago

Hi, I ran BRAKER with docker, but an error was occurred. Here are the run logs:

[WARN tini (101094)] Tini is not running as PID 1 and isn't registered as a child subreaper. Zombie processes will not be re-parented to Tini, so zombie reaping won't work. To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1. Sat Dec 30 05:22:41 2023:Both protein and RNA-Seq data in input detected. BRAKER will be executed in ETP mode (BRAKER3).

                           BRAKER CONFIGURATION

BRAKER CALL: /opt/BRAKER/scripts/braker.pl --species=WFhap1 --gff3 --threads=8 --genome=/gDir/WFhap1.simple_mask.soft.complex_mask.hard.fasta --bam=/tDir/WFhap1.CF.mask.sort.bam,/tDir/WFhap1.mask.sort.bam --prot_seq=/pDir/citrus_prot.fa Sat Dec 30 05:22:41 2023: braker.pl version 3.0.6 Sat Dec 30 05:22:41 2023:Both protein and RNA-Seq data in input detected. BRAKER will be executed in ETP mode (BRAKER3).

Sat Dec 30 05:22:41 2023: Configuring of BRAKER for using external tools... Sat Dec 30 05:22:41 2023: Trying to set $AUGUSTUS_CONFIG_PATH... Sat Dec 30 05:22:41 2023: Found environment variable $AUGUSTUS_CONFIG_PATH. Sat Dec 30 05:22:41 2023: Checking /usr/share/augustus/config/ as potential path for $AUGUSTUS_CONFIG_PATH. Sat Dec 30 05:22:41 2023: Success! Setting $AUGUSTUS_CONFIG_PATH to /usr/share/augustus/config/! Sat Dec 30 05:22:41 2023: Trying to set $AUGUSTUS_BIN_PATH... Sat Dec 30 05:22:41 2023: Found environment variable $AUGUSTUS_BIN_PATH. Sat Dec 30 05:22:41 2023: Checking /usr/bin/ as potential path for $AUGUSTUS_BIN_PATH. Sat Dec 30 05:22:41 2023: Success! Setting $AUGUSTUS_BIN_PATH to /usr/bin/! Sat Dec 30 05:22:41 2023: Trying to set $AUGUSTUS_SCRIPTS_PATH... Sat Dec 30 05:22:41 2023: Found environment variable $AUGUSTUS_SCRIPTS_PATH. Sat Dec 30 05:22:41 2023: Checking /usr/share/augustus/scripts/ as potential path for $AUGUSTUS_SCRIPTS_PATH. Sat Dec 30 05:22:41 2023: Success! Setting $AUGUSTUS_SCRIPTS_PATH to /usr/share/augustus/scripts/! Sat Dec 30 05:22:41 2023: Trying to set $PYTHON3_PATH... Sat Dec 30 05:22:41 2023: Did not find environment variable $PYTHON3_PATH. Sat Dec 30 05:22:41 2023: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH Sat Dec 30 05:22:41 2023: Checking /opt/conda/bin as potential path for $PYTHON3_PATH. Sat Dec 30 05:22:41 2023: Success! Setting $PYTHON3_PATH to /opt/conda/bin! Sat Dec 30 05:22:41 2023: Trying to set $GENEMARK_PATH... Sat Dec 30 05:22:41 2023: Found environment variable $GENEMARK_PATH. Sat Dec 30 05:22:41 2023: Checking /opt/ETP/bin as potential path for $GENEMARK_PATH. Sat Dec 30 05:22:41 2023: Success! Setting $GENEMARK_PATH to /opt/ETP/bin! Sat Dec 30 05:22:41 2023: Trying to set $BAMTOOLS_PATH... Sat Dec 30 05:22:41 2023: Did not find environment variable $BAMTOOLS_PATH. Sat Dec 30 05:22:41 2023: Trying to guess BAMTOOLS_PATH from location of bamtools executable that is available in your $PATH Sat Dec 30 05:22:41 2023: Checking /usr/bin as potential path for $BAMTOOLS_PATH. Sat Dec 30 05:22:41 2023: Success! Setting $BAMTOOLS_PATH to /usr/bin! Sat Dec 30 05:22:41 2023: Trying to set $SAMTOOLS_PATH... Sat Dec 30 05:22:41 2023: Did not find environment variable $SAMTOOLS_PATH. Sat Dec 30 05:22:42 2023: Trying to guess SAMTOOLS_PATH from location of samtools executable that is available in your $PATH Sat Dec 30 05:22:42 2023: Checking /usr/bin as potential path for $SAMTOOLS_PATH. Sat Dec 30 05:22:42 2023: Success! Setting $SAMTOOLS_PATH to /usr/bin! Sat Dec 30 05:22:42 2023: Trying to set $DIAMOND_PATH... Sat Dec 30 05:22:42 2023: Did not find environment variable $DIAMOND_PATH. Sat Dec 30 05:22:43 2023: Trying to guess DIAMOND_PATH from location of diamond executable that is available in your $PATH Sat Dec 30 05:22:43 2023: Checking /opt/ETP/tools as potential path for $DIAMOND_PATH. Sat Dec 30 05:22:43 2023: Success! Setting $DIAMOND_PATH to /opt/ETP/tools! Sat Dec 30 05:22:43 2023: Trying to set $PROTHINT_PATH... Sat Dec 30 05:22:43 2023: Did not find environment variable $PROTHINT_PATH. Sat Dec 30 05:22:43 2023: Trying to guess PROTHINT_PATH from location of prothint.py executable that is available in your $PATH Sat Dec 30 05:22:43 2023: Checking /opt/ETP/bin/gmes/ProtHint/bin as potential path for $PROTHINT_PATH. Sat Dec 30 05:22:43 2023: Success! Setting $PROTHINT_PATH to /opt/ETP/bin/gmes/ProtHint/bin! Sat Dec 30 05:22:43 2023: Trying to set $TSEBRA_PATH... Sat Dec 30 05:22:43 2023: Did not find environment variable $TSEBRA_PATH. Sat Dec 30 05:22:43 2023: Trying to guess TSEBRA_PATH from location of tsebra.py executable that is available in your $PATH Sat Dec 30 05:22:43 2023: Checking /opt/TSEBRA/bin as potential path for $TSEBRA_PATH. Sat Dec 30 05:22:43 2023: Success! Setting $TSEBRA_PATH to /opt/TSEBRA/bin! Sat Dec 30 05:22:43 2023: Trying to set $CDBTOOLS_PATH... Sat Dec 30 05:22:43 2023: Did not find environment variable $CDBTOOLS_PATH. Sat Dec 30 05:22:43 2023: Trying to guess CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH Sat Dec 30 05:22:43 2023: Checking /opt/cdbfasta as potential path for $CDBTOOLS_PATH. Sat Dec 30 05:22:43 2023: Success! Setting $CDBTOOLS_PATH to /opt/cdbfasta! Sat Dec 30 05:22:56 2023: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 2544 bamtools not installed. Please install it first. Warning: this container exposes TCP/IP ports

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  • STARTING 7a6aaf49-d7df-3595-9e64-d822aab2f3b5 *
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    executing: tini

How to fix it, please give me some suggestions. Thanks very much.

KatharinaHoff commented 8 months ago

bamtools are in the container installed at /usr/bin/bamtools . I am surprised that this is not automatically detected. I am routinely running the container in Singularity and never had this problem. set the braker.pl option --BAMTOOLS_PATH=/usr/bin/

leon945945 commented 8 months ago

Thanks for your solution, I'll set the option and try again.

leon945945 commented 8 months ago

Hi, I added the --BAMTOOLS_PATH parameter, but still coccurred the same error. Bamtools not found.

leon945945 commented 8 months ago

Hi, I have tried to run braker with singularity, it runs OK at present.

A little confused question is that I have assigned the parameter --workingdir a certain directory, but brakeroutputs intermediate results to ~/braker. Under this situation, what makes me worried is that if I run another braker program with singularity, it still outputs intermediate results to ~/braker, the results of previous braker program will be covered and influenced. How can I run anther braker program with singularity.

leon945945 commented 8 months ago

I found the reason that braker outputs results to ~/braker, the --workingdir I mounted to container that braker can not find, I changed the mounted directory to the same path name with host directory, then braker could output results to --workingdir.

KatharinaHoff commented 7 months ago

I assume that this issue is solved. I confirmed that bamtools is installed and available in the latest docker container.