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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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Error in braker.pl at line 5473, .gm_key is up to date, but GeneMark-ETP still doesn't work #749

Closed jkmh2 closed 8 months ago

jkmh2 commented 8 months ago

**Hi there,

I was running BRAKER3 (short-read RNA and protein data) and it ran into problems during the gmetp.pl step. Here is the last entry in braker.log:**

Tue Jan 23 14:09:58 2024: Running gmetp.pl

/usr/bin/perl /opt/GeneMark-ETP-main/bin/gmetp.pl --cfg /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_config.yaml --workdir /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMar k-ETP --bam /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stdout 2>/home/jkmh2/US DA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stderr

Here is the error from the bash command line: ERROR in file /opt/BRAKER-3.0.3/scripts/braker.pl at line 5473 Failed to execute: /usr/bin/perl /opt/GeneMark-ETP-main/bin/gmetp.pl --cfg /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_config.yaml --workdir /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP --bam /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stdout 2>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stderr Failed to execute: /usr/bin/perl /opt/GeneMark-ETP-main/bin/gmetp.pl --cfg /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_config.yaml --workdir /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP --bam /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stdout 2>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stderr The most common problem is an expired or not present file ~/.gm_key or that GeneMark-ETP didn't receive enough evidence from the input data, in this case, see errors/GeneMark-ETP.stderr!

Here is the GeneMark-ETP.stderr: error, file/folder not found: /home/jkmh2/USDA_OmykA_1.1/Practice_Jan_22_2024/braker/GeneMarkETP/ rnaseq/hisat2/mapping_ERX4030517_OmykA_1.1_sorted.bam

In the "GeneMark-ETP" directory, the "etp_data" directory is empty.
In /GeneMark-ETP/rnaseq/hisat2 there are bunch of sorted.bam files listed: mapping_ERX4030517_OmykA_1.1_sorted.bam mapping_ERX4030524_OmykA_1.1_sorted.bam mapping_SRX2894150_OmykA_1.1_sorted.bam mapping_SRX2894156_OmykA_1.1_sorted.bam mapping_SRX2894162_OmykA_1.1_sorted.bam mapping_ERX4030518_OmykA_1.1_sorted.bam mapping_ERX4030526_OmykA_1.1_sorted.bam mapping_SRX2894151_OmykA_1.1_sorted.bam mapping_SRX2894157_OmykA_1.1_sorted.bam mapping_SRX2894163_OmykA_1.1_sorted.bam mapping_ERX4030519_OmykA_1.1_sorted.bam mapping_ERX4030527_OmykA_1.1_sorted.bam mapping_SRX2894152_OmykA_1.1_sorted.bam mapping_SRX2894158_OmykA_1.1_sorted.bam mapping_SRX2894164_OmykA_1.1_sorted.bam mapping_ERX4030520_OmykA_1.1_sorted.bam mapping_ERX4030528_OmykA_1.1_sorted.bam mapping_SRX2894153_OmykA_1.1_sorted.bam mapping_SRX2894159_OmykA_1.1_sorted.bam mapping_ERX4030521_OmykA_1.1_sorted.bam mapping_ERX4030529_OmykA_1.1_sorted.bam mapping_SRX2894154_OmykA_1.1_sorted.bam mapping_SRX2894160_OmykA_1.1_sorted.bam mapping_ERX4030523_OmykA_1.1_sorted.bam mapping_ERX4030530_OmykA_1.1_sorted.bam mapping_SRX2894155_OmykA_1.1_sorted.bam mapping_SRX2894161_OmykA_1.1_sorted.bam

However, when you try to access the BAM files it says: more: cannot open mapping_ERX4030517_OmykA_1.1_sorted.bam: No such file or directory

**It seems like there was a problem with mapping the BAM files.

Even though my .gm_key was not expired, I updated it anyway. BRAKER still gave the error listed above. Here are some commands that show that I am up to date with GeneMark-ES:**

$ which gmes_petap.pl /opt/gmes_linux_64_4/gmes_petap.pl

$ ./check_install.bash Checking GeneMark-ES installation Checking Perl setup All required Perl modules were found Checking GeneMark.hmm setup GeneMark.hmm was found GeneMark.hmm is set GeneMark.hmm is executable Performing GeneMark.hmm test run All required components for GeneMark-ES were found

**Please help! I've run out of ideas of what to do.

Thank you, Johnny**

KatharinaHoff commented 8 months ago

Please update BRAKER and its dependencies. The key dependency including that error message was removed last year. I recommend the singularity container.

jkmh2 @.***> schrieb am Di. 23. Jan. 2024 um 21:51:

**Hi there,

I was running BRAKER3 (short-read RNA and protein data) and it ran into problems during the gmetp.pl step. Here is the last entry in braker.log:** Tue Jan 23 14:09:58 2024: Running gmetp.pl

/usr/bin/perl /opt/GeneMark-ETP-main/bin/gmetp.pl --cfg /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_config.yaml --workdir /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMar k-ETP --bam /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stdout 2>/home/jkmh2/US DA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stderr

Here is the error from the bash command line: ERROR in file /opt/BRAKER-3.0.3/scripts/braker.pl at line 5473 Failed to execute: /usr/bin/perl /opt/GeneMark-ETP-main/bin/gmetp.pl --cfg /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_config.yaml --workdir /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP --bam /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stdout 2>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stderr Failed to execute: /usr/bin/perl /opt/GeneMark-ETP-main/bin/gmetp.pl --cfg /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_config.yaml --workdir /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP --bam /home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stdout 2>/home/jkmh2/USDA_OmykA_1.1/Practice2_Jan_22_2024/braker/errors/GeneMark-ETP.stderr The most common problem is an expired or not present file ~/.gm_key or that GeneMark-ETP didn't receive enough evidence from the input data, in this case, see errors/GeneMark-ETP.stderr!

Here is the GeneMark-ETP.stderr: error, file/folder not found: /home/jkmh2/USDA_OmykA_1.1/Practice_Jan_22_2024/braker/GeneMarkETP/ rnaseq/hisat2/mapping_ERX4030517_OmykA_1.1_sorted.bam

In the "GeneMark-ETP" directory, the "etp_data" directory is empty. In /GeneMark-ETP/rnaseq/hisat2 there are bunch of sorted.bam files listed: mapping_ERX4030517_OmykA_1.1_sorted.bam mapping_ERX4030524_OmykA_1.1_sorted.bam mapping_SRX2894150_OmykA_1.1_sorted.bam mapping_SRX2894156_OmykA_1.1_sorted.bam mapping_SRX2894162_OmykA_1.1_sorted.bam mapping_ERX4030518_OmykA_1.1_sorted.bam mapping_ERX4030526_OmykA_1.1_sorted.bam mapping_SRX2894151_OmykA_1.1_sorted.bam mapping_SRX2894157_OmykA_1.1_sorted.bam mapping_SRX2894163_OmykA_1.1_sorted.bam mapping_ERX4030519_OmykA_1.1_sorted.bam mapping_ERX4030527_OmykA_1.1_sorted.bam mapping_SRX2894152_OmykA_1.1_sorted.bam mapping_SRX2894158_OmykA_1.1_sorted.bam mapping_SRX2894164_OmykA_1.1_sorted.bam mapping_ERX4030520_OmykA_1.1_sorted.bam mapping_ERX4030528_OmykA_1.1_sorted.bam mapping_SRX2894153_OmykA_1.1_sorted.bam mapping_SRX2894159_OmykA_1.1_sorted.bam mapping_ERX4030521_OmykA_1.1_sorted.bam mapping_ERX4030529_OmykA_1.1_sorted.bam mapping_SRX2894154_OmykA_1.1_sorted.bam mapping_SRX2894160_OmykA_1.1_sorted.bam mapping_ERX4030523_OmykA_1.1_sorted.bam mapping_ERX4030530_OmykA_1.1_sorted.bam mapping_SRX2894155_OmykA_1.1_sorted.bam mapping_SRX2894161_OmykA_1.1_sorted.bam

However, when you try to access the BAM files it says: more: cannot open mapping_ERX4030517_OmykA_1.1_sorted.bam: No such file or directory

**It seems like there was a problem with mapping the BAM files.

Even though my .gm_key was not expired, I updated it anyway. BRAKER still gave the error listed above. Here are some commands that show that I am up to date with GeneMark-ES:**

$ which gmes_petap.pl /opt/gmes_linux_64_4/gmes_petap.pl

$ ./check_install.bash Checking GeneMark-ES installation Checking Perl setup All required Perl modules were found Checking GeneMark.hmm setup GeneMark.hmm was found GeneMark.hmm is set GeneMark.hmm is executable Performing GeneMark.hmm test run All required components for GeneMark-ES were found

**Please help! I've run out of ideas of what to do.

Thank you, Johnny**

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jkmh2 commented 8 months ago

Thank you for the suggestion. I got BRAKER to run. Closing the issue now.