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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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Using Iso-seq data for Braker annotation #863

Open Upendra19993 opened 5 days ago

Upendra19993 commented 5 days ago

Hi, I am trying to use iso-seq data for braker annotation. When I passed the job, within 30mins, I get an error.

I have attached the error here for your reference. Kindly let me know how to resolve this issue.

(base) [uqwwijes@bun113 braker3]$ singularity exec /scratch/project/qaafi-cnafs/braker3/braker3_lr.sif braker.pl --genome=M.indica_KP_genome.fasta.masked.fa --bam=KP_combined_SQANTI_uf_hq.bam --workingdir=KP_SQANTIBraker_sifrun3 --threads 24 --gff3 --softmasking --AUGUSTUS_CONFIG_PATH=/scratch/project/qaafi-cnafs/braker3/config # Tue Sep 24 06:45:24 2024: Log information is stored in file /scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/braker.log ERROR in file /opt/BRAKER/scripts/braker.pl at line 6291 Failed to execute: /opt/Augustus/bin//etraining --species=Sp_225 --AUGUSTUS_CONFIG_PATH=/scratch/project/qaafi-cnafs/braker3/config /scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/train.f.gb 1> /scratch/project_mnt/S0030/braker3/KP_SQANTIBraker_sifrun3/gbFilterEtraining.stdout 2>/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/errors/gbFilterEtraining.stderr****

The log file information also has attached. braker.log

Thank you very much!

Kind regards, Upendra.

KatharinaHoff commented 4 days ago

What is the content of these files?

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/gbFilterEtraining.stdout

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/errors/gbFilterEtraining.stderr

If there is a segmentation fault in the stderr file, please share (e.g. via e-mail):

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/train.f.gb

Upendra19993 commented 4 days ago

Hi KatharinaHoff,

I have difficulties to attach the files you mentioned to this, but I have attached them and some other files saved in the 'error ' directory via an email.

Thank you very much!

Kind regards, Upendra.

Upendra19993 commented 4 days ago

Hi Katharina Hoff,

Herewith, I have attached the gbFilterEtraining.stdout and train.f.gb files for your kind consideration.

The gbFilterEtraining.stderr you have mentioned is empty.

There are other files which have been saved under a directory names as 'error'. They all are empty.

Though the job ended without completing the whole process, there are some output files. Kindly let me know if it is good to have a look, I will share the files with you.

Thank you very much!

Best regards, Upendra. gbFilterEtraining.stdout https://drive.google.com/file/d/1GJdGiFxA67FZInPqlsbFwMDE-hICcrOS/view?usp=drive_web train.f.gb https://drive.google.com/file/d/1hZXHat9EWtbzsremIunvHJFboAe81hMi/view?usp=drive_web

On Tue, Sep 24, 2024 at 8:26 PM Katharina Hoff @.***> wrote:

What is the content of these files?

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/gbFilterEtraining.stdout

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/errors/gbFilterEtraining.stderr

If there is a segmentation fault in the stderr file, please share (e.g. via e-mail):

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/train.f.gb

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/863#issuecomment-2370878395, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWXPDELSWR2XHJAGD2SEJ43ZYE46PAVCNFSM6AAAAABOW74Q3WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZQHA3TQMZZGU . You are receiving this because you authored the thread.Message ID: @.***>

Upendra19993 commented 4 days ago

gbFilterEtraining.stdout https://drive.google.com/file/d/1rl9g_eL_Y7xcX_HLkHumYc_FIzuWnVe0/view?usp=drive_web train.f.gb https://drive.google.com/file/d/1eGbcBiUFhxKujiy94DZM6gPY2r7uXJB2/view?usp=drive_web Hi Katharina Hoff,

I am sending the two files I attached to the previous email again for your reference. Let me know whether you have access to these files.

Thank you! Kind regards, Upendra.

On Wed, Sep 25, 2024 at 3:00 AM Upendra wijesundara < @.***> wrote:

Hi Katharina Hoff,

Herewith, I have attached the gbFilterEtraining.stdout and train.f.gb files for your kind consideration.

The gbFilterEtraining.stderr you have mentioned is empty.

There are other files which have been saved under a directory names as 'error'. They all are empty.

Though the job ended without completing the whole process, there are some output files. Kindly let me know if it is good to have a look, I will share the files with you.

Thank you very much!

Best regards, Upendra. gbFilterEtraining.stdout https://drive.google.com/file/d/1GJdGiFxA67FZInPqlsbFwMDE-hICcrOS/view?usp=drive_web train.f.gb https://drive.google.com/file/d/1hZXHat9EWtbzsremIunvHJFboAe81hMi/view?usp=drive_web

On Tue, Sep 24, 2024 at 8:26 PM Katharina Hoff @.***> wrote:

What is the content of these files?

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/gbFilterEtraining.stdout

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/errors/gbFilterEtraining.stderr

If there is a segmentation fault in the stderr file, please share (e.g. via e-mail):

/scratch/project_mnt/S0030/braker3/KP_SQANTI__Braker_sifrun3/train.f.gb

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/863#issuecomment-2370878395, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWXPDELSWR2XHJAGD2SEJ43ZYE46PAVCNFSM6AAAAABOW74Q3WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZQHA3TQMZZGU . You are receiving this because you authored the thread.Message ID: @.***>

KatharinaHoff commented 9 hours ago

I have checked the train.f.gb file. It does not lead to etraining problems. Possibly, your species parameters are corrupt. If you could make them available, I could also have a look at them. I need the entire contents of the folder /scratch/project/qaafi-cnafs/braker3/config/species/Sp_225

Upendra19993 commented 5 hours ago

Hi Katharina,

I checked the folder /scratch/project/qaafi-cnafs/braker3/config/species/. But within the species folder, no folder is created for Sp_225. Kindly let me know how I can support you to find the error.

Thank you very much!

Best regards, Upendra.

On Sun, Sep 29, 2024 at 3:58 AM Katharina Hoff @.***> wrote:

I have checked the train.f.gb file. It does not lead to etraining problems. Possibly, your species parameters are corrupt. If you could make them available, I could also have a look at them. I need the entire contents of the folder /scratch/project/qaafi-cnafs/braker3/config/species/Sp_225

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/863#issuecomment-2380848941, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWXPDEOMY3TYW3OTNFW35BLZY3U3VAVCNFSM6AAAAABOW74Q3WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBQHA2DQOJUGE . You are receiving this because you authored the thread.Message ID: @.***>