Problems in RUNNING GENEMARK-EX #716
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What is inside your protein file? Is it a an OrthoDB partition? You have to
provide a protein file with a large degree of redundancy in protein space,
i.e. the proteins should come from one species, only.
…On Thu, Dec 7, 2023 at 4:03 AM ChuanzhengWei ***@***.***> wrote:
Dear Braker team,
I got an error when using brake3 built by Singularity for gene prediction.
I am not sure whether there is a problem with gmetp.pl during the running
process. My input file is a protein file and a bam file aligned with hisat2.
This is my input command:
singularity exec /public/home/weichuanzheng/software/singularity/braker3/braker3.sif braker.pl --JAVA_PATH=/public/home/weichuanzheng/software/jdk/bin --threads=8 --species=s349 \
--genome=/public/home/weichuanzheng/project/08.pangenome/03.mask/s349/s349.nextpolish.fasta.masked \
--prot_seq=/public/home/weichuanzheng/project/11.Sorghum_genome/06.prot/structure_annotation1.fasta \
--bam==/public/home/weichuanzheng/project/08.pangenome/03.mask/s349/bamfile/SRR23260553.sorted.bam,............
The following is the specific content of the error report:
In 'braker.log':
# Wed Dec 6 10:37:36 2023: sorting RNA-Seq BAM files
# Wed Dec 6 12:42:05 2023: Running gmetp.pl
/usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /public/home/weichuanzheng/project/08.pangenome/03.mask/s349/annotation/braker/GeneMark-ETP/etp_config.yaml --workdir /public/home/weichuanzheng/project/08.pangenome/03.mask/s349/annotation/braker/GeneMark-ETP --bam /public/home/weichuanzheng/project/08.pangenome/03.mask/s349/annotation/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask 1>/public/home/weichuanzheng/project/08.pangenome/03.mask/s349/annotation/braker/errors/GeneMark-ETP.stdout 2>/public/home/weichuanzheng/project/08.pangenome/03.mask/s349/annotation/braker/errors/GeneMark-ETP.stderr
At the end of 'GeneMark-ETP.stderr':
WARNING: 'ptg000031l_np1212' does not match any sequence in the fasta file. Maybe the two files do not belong together.
error
error, file/folder not found: transcripts_merged.fasta.gff
In 'GeneMark-ETP.stdout':
GeneMarkS: error on last system call, error code 256
Abort program!!!
I would appreciate any suggestions.
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My protein file includes sequences from 60 varieties of sorghum, one variety of rice, and one variety of maize. Initially, I faced a problem that did not seem to stem from the protein file itself. After renaming and shortening the headers of the sequences in the genome file, I successfully generated the braker.gff file. However, I've encountered a new challenge: the generated GFF file does not contain UTRs (Untranslated Regions). I think this issue might be related to the limitations of the container environment, as I am running BRAKER through Singularity due to the lack of root privileges on my system. Given these constraints, could you please advise on how I might obtain a GFF file that includes UTRs? Any guidance or suggestions you can offer would be greatly appreciated, as this is a critical component of my project. Thank you in advance for your time and assistance. I look forward to your valuable input. Best regards |
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This is the version I'm using |
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See #587 |
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I did not find GeneMark-ETP/rnaseq/stringtie/transcripts_merged.gff, so I need to reuse stringtie to obtain a new gff file, and then merge the stringtie.gff and braker.gtf files through stringtie2utr.py?
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Yes, you need to run stringtie. The script is not connected to BRAKER, yet. |
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thank you, I successfully obtained a GTF file containing UTRs using stringtie2utr.py, but I've encountered a new issue: there are multiple pieces of information generated for the 5' UTR or 3' UTR of the same gene.like this I want to know if this situation is normal. |
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This is not necessarily wrong. UTRs can be spliced
ChuanzhengWei ***@***.***> schrieb am Mi. 13. Dez. 2023 um
09:57:
… thank you, I successfully obtained a GTF file containing UTRs using
stringtie2utr.py, but I've encountered a new issue: there are multiple
pieces of information generated for the 5' UTR or 3' UTR of the same
gene.like this
178 Chr01 stringtie2utr five_prime_UTR 36899 36899 1000 - . transcript_id "g4.t2"; gene_id "g4";
179 Chr01 stringtie2utr five_prime_UTR 37358 37440 1000 - . transcript_id "g4.t2"; gene_id "g4";
180 Chr01 stringtie2utr five_prime_UTR 41705 41825 1000 - . transcript_id "g4.t2"; gene_id "g4";
181 Chr01 stringtie2utr five_prime_UTR 42029 42456 1000 - . transcript_id "g4.t2"; gene_id "g4"
I want to know if this situation is normal.
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Dear Braker team,
I got an error when using brake3 built by Singularity for gene prediction. I am not sure whether there is a problem with gmetp.pl during the running process. My input file is a protein file and a bam file aligned with hisat2.
This is my input command:
The following is the specific content of the error report:
In 'braker.log':
At the end of 'GeneMark-ETP.stderr':
In 'GeneMark-ETP.stdout':
I would appreciate any suggestions.
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