/gannet/Atumefaciens/20190701_pgen_maker_v074_annotation/

MAKER annotation of the Panopea generosa Pgenerosa_v074 genome assembly. This assembly is a subset of Pgenerosa_v070 containing the longest 18 scaffolds in the assembly. This was run on Mox. See notebook entry (link at bottom of this file) for details on input files used to run this annotation.

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FILES

- 20190701_pgen_maker_v074_annotation.sh: SBATCH script to run MAKER on Mox.

- blastp_annotation: Folder containing BLASTp output from MAKER.

- _Inline: ?

- interproscan_annotation: Folder containing InterProscan output from MAKER.

- maker_bopts.ctl: Control file generated by MAKER.

- maker_exe.ctl: Control file generated by MAKER.

- maker_opts.ctl: Control file containing all the options/input files for MAKER to run.

- Pgenerosa_v074.all.gff: Initial GFF produced by MAKER's gene predictions.

- Pgenerosa_v074.all.maker.proteins.fasta: Initial FastA containing protein sequences identified by MAKER gene predictions.

- Pgenerosa_v074.all.maker.transcripts.fasta:  Initial FastA containing transcript sequences identified by MAKER gene predictions.

- Pgenerosa_v074_genome_snap02.all.maker.proteins.renamed.putative_function.fasta: Final FastA of protein sequences predicted after MAKER and two rounds of SNAP.

- Pgenerosa_v074_genome_snap02.all.maker.transcripts.renamed.putative_function.fasta: Final FastA of transcript sequences predicted after MAKER and two rounds of SNAP.

- Pgenerosa_v074_genome_snap02.all.renamed.putative_function.domain_added.gff: "Canonical" annotation GFF produced after MAKER and two rounds of SNAP. Contains putative functional annotations, protein domain annotations, and gene ontology (GO) terms. NOTE: Contains corresponding FastA sequences after standard GFF data.

- Pgenerosa_v074_genome_snap02.all.renamed.putative_function.gff: Annotation GFF produced after MAKER and two rounds of SNAP. Contains putative functional annotations. NOTE: Contains corresponding FastA sequences after standard GFF data.

- Pgenerosa_v074_genome_snap02.all.renamed.visible_ips_domains.gff: InterProscan domain GFF. Useful for some genome browsers (e.g. Apollo).

- Pgenerosa_v074.maker.all.noseqs.est2genome.gff: Initial GFF of EST alignments produced by MAKER. Used as EST evidence for two subsequent rounds of SNAP gene prediction. Does not contain corresponding FastA sequences at the end of the file.

- Pgenerosa_v074.maker.all.noseqs.gff: Initial GFF produced by MAKER. Does not contain corresponding FastA sequences at the end of the file.

- Pgenerosa_v074.maker.all.noseqs.protein2genome.gff:  Initial GFF of protein alignments produced by MAKER. Used as EST evidence for two subsequent rounds of SNAP gene prediction. Does not contain corresponding FastA sequences at the end of the file.

- Pgenerosa_v074.maker.all.noseqs.repeats.gff:  Initial GFF of repeats alignments produced by MAKER. Used as EST evidence for two subsequent rounds of SNAP gene prediction. Does not contain corresponding FastA sequences at the end of the file.

- Pgenerosa_v074.maker.output: MAKER "working directory". Contains all intermediate files/folders produced by MAKER.

- slurm-997700.out: SLURM output file (i.e. stderr/stdout).

- snap*: "Working directories" used by each round of SNAP gene prediction. Contains all the intermediate files/folders produced by SNAP/MAKER.

- system_path.log: Contents of Sam's system $PATH on Mox.


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Notebook:

https://robertslab.github.io/sams-notebook/2019/07/01/Genome-Annotation-Pgenerosa_v074-MAKER-on-Mox.html