Commit 150450ba authored by Matthew Berkeley's avatar Matthew Berkeley

BUSCO 4.0.5

parent 2be0a934
4.0.5
- Constrain to use Augustus v3.2.3 on conda and Docker
4.0.4
- Fix inefficiency introduced in 4.0.3
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......@@ -23,14 +23,17 @@ export BUSCO_CONFIG_FILE="/path/to/myconfig.ini"
If you have trouble installing one of the many third-party tools, try the official Docker container: https://hub.docker.com/r/ezlabgva/busco/tags
***Note regarding Augustus version:**
If using BUSCO on eukaryota genomes, Augustus is the gene predictor used. We have noticed significant discrepancies between the results using Augustus v3.3.x and v3.2.x.
Until this is resolved, we recommend using Augustus v3.2.3.*
Report problems on the BUSCO issue board at https://gitlab.com/ezlab/busco/issues
To get help on BUSCO use: ``busco -h`` and ``python3 scripts/generate_plot.py -h``
**!!!** Don't use "odb9" datasets with BUSCOv4. If you need to reproduce previous analyses, use BUSCOv3 (https://gitlab.com/ezlab/busco/-/tags/3.0.2)
Note: Use Augustus version 3.2.3, as we noticed that with Augustus version 3.3 there is a problem with the etraining step for some genomes.
Note: For v4.0.2 and before, when running auto-lineage, the initial results for eukaryotes were incomplete. This was
deliberate, as these initial results are used merely to determine whether the genome scores highest against the
bacteria, archaea or eukaryota datasets. If the eukaryota dataset was selected, BUSCO then attempts to place the input
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......@@ -247,9 +247,9 @@ class BuscoLogger(logging.getLoggerClass()):
self._err_hdlr.setFormatter(self._normal_formatter)
self.addHandler(self._err_hdlr)
# Random id used in filename to avoid complications for parallel BUSCO runs.
if not os.access(os.getcwd(), os.W_OK):
raise SystemExit("No permission to write in the current directory.")
# Random id used in filename to avoid complications for parallel BUSCO runs.
self._file_hdlr = logging.FileHandler("busco_{}.log".format(type(self).random_id), mode="a")
self._file_hdlr.setLevel(logging.DEBUG)
self._file_hdlr.setFormatter(self._verbose_formatter)
......
......@@ -1157,8 +1157,8 @@ class TBLASTNRunner:
if append_busco_coords:
coords[busco_name][contig]["busco_coords"].append([busco_start, busco_end])
if blast_eval < coords[busco_name][contig]["blast_eval"]:
coords[busco_name][contig]["blast_eval"] = blast_eval
if blast_eval < coords[busco_name][contig]["blast_eval"]:
coords[busco_name][contig]["blast_eval"] = blast_eval
return coords
......
......@@ -430,7 +430,7 @@ class GenomeAnalysisEukaryotes(GenomeAnalysis):
logger.info("All files converted to short genbank files, now running the training scripts")
new_species_name = self._run_new_species()
self._target_species = new_species_name
self._target_species = new_species_name # todo: check new species folder can be read/written - detect any silent Augustus issues
self._merge_gb_files()
......
......@@ -6,4 +6,4 @@ Copyright (c) 2016-2020, Evgeny Zdobnov ([email protected])
Licensed under the MIT license. See LICENSE.md file.
"""
__version__ = "4.0.4"
__version__ = "4.0.5"
INFO: ***** Start a BUSCO v4.0.4 analysis, current time: 02/12/2020 16:38:00 *****
INFO: ***** Start a BUSCO v4.0.5 analysis, current time: 02/12/2020 16:38:00 *****
INFO: Configuring BUSCO with /busco/config/config.ini
INFO: Mode is genome
INFO: Input file is genome.fna
......
INFO: ***** Start a BUSCO v4.0.4 analysis, current time: 02/12/2020 16:40:52 *****
INFO: ***** Start a BUSCO v4.0.5 analysis, current time: 02/12/2020 16:40:52 *****
INFO: Configuring BUSCO with /busco/config/config.ini
INFO: Mode is genome
INFO: Input file is genome.fna
......
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