[med-svn] [Git][med-team/busco][master] 5 commits: New upstream version 5.4.3
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Aug 23 16:01:03 BST 2022
Andreas Tille pushed to branch master at Debian Med / busco
Commits:
ac7856a5 by Andreas Tille at 2022-08-23T16:25:30+02:00
New upstream version 5.4.3
- - - - -
b59ae1be by Andreas Tille at 2022-08-23T16:36:54+02:00
New upstream version 5.4.3
- - - - -
402a52da by Andreas Tille at 2022-08-23T16:36:57+02:00
Update upstream source from tag 'upstream/5.4.3'
Update to upstream version '5.4.3'
with Debian dir 12221e564a9b2d97cfc28cb23ff9a9b5799c42bd
- - - - -
de329d78 by Andreas Tille at 2022-08-23T16:41:57+02:00
DEP3
- - - - -
74b73f5e by Andreas Tille at 2022-08-23T16:43:18+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- CHANGELOG
- debian/changelog
- debian/patches/find-bbmap-instead-of-bbtools.patch
- src/busco/_version.py
- src/busco/busco_tools/augustus.py
- src/busco/busco_tools/metaeuk.py
- test_data/bacteria/expected_log.txt
- test_data/eukaryota/expected_log.txt
Changes:
=====================================
CHANGELOG
=====================================
@@ -1,3 +1,6 @@
+5.4.3
+- Fix bug in augustus --long pipeline (Issue #586)
+
5.4.2
- Fix batch summary statistics reporting bug in eukaryote pipeline
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+busco (5.4.3-1) unstable; urgency=medium
+
+ * New upstream version
+ * DEP3
+
+ -- Andreas Tille <tille at debian.org> Tue, 23 Aug 2022 16:42:14 +0200
+
busco (5.4.2+ds-1) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/find-bbmap-instead-of-bbtools.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Nilesh Patra
+Last-Update: 2022-07-29 19:08:42 +0530
+Description: use bbmap instead of bbtools
+
--- a/config/config.ini
+++ b/config/config.ini
@@ -108,6 +108,6 @@
=====================================
src/busco/_version.py
=====================================
@@ -6,4 +6,4 @@ Copyright (c) 2016-2022, Evgeny Zdobnov (ez at ezlab.org)
Licensed under the MIT license. See LICENSE.md file.
"""
-__version__ = "5.4.2"
+__version__ = "5.4.3"
=====================================
src/busco/busco_tools/augustus.py
=====================================
@@ -812,9 +812,9 @@ class OptimizeAugustusRunner(BaseRunner):
self.new_species_name = None
def configure_runner(self, output_folder, new_species_name):
+ self._output_folder = output_folder
super().configure_runner()
self.run_number += 1
- self._output_folder = output_folder
self.training_set_db = os.path.join(self._output_folder, "training_set.db")
self.new_species_name = new_species_name
=====================================
src/busco/busco_tools/metaeuk.py
=====================================
@@ -707,8 +707,14 @@ class MetaeukRunner(BaseRunner):
raise NoRerunFile
def write_gff_files(self, sc_folder, mc_folder, frag_folder):
- with open(self.gff_file, "r") as gf:
- lines = gf.readlines()
+ try:
+ with open(self.gff_file, "r") as gf:
+ lines = gf.readlines()
+ except FileNotFoundError:
+ logger.warning(
+ "Metaeuk did not create a GFF file. Please use Metaeuk version 5-34c21f2 or higher for GFF results."
+ )
+ return
id_pattern = re.compile(r".*Target_ID=(.*?)[_;]")
current_busco = ""
=====================================
test_data/bacteria/expected_log.txt
=====================================
@@ -1,122 +1,118 @@
-2022-07-15 15:17:48 INFO: ***** Start a BUSCO v5.4.2 analysis, current time: 07/15/2022 15:17:48 *****
-2022-07-15 15:17:48 INFO: Configuring BUSCO with local environment
-2022-07-15 15:17:48 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
-2022-07-15 15:17:48 INFO: Mode is genome
-2022-07-15 15:17:48 INFO: Downloading information on latest versions of BUSCO data...
-2022-07-15 15:18:00 INFO: Input file is /busco_wd/test_data/bacteria/genome.fna
-2022-07-15 15:18:00 INFO: No lineage specified. Running lineage auto selector.
+2022-08-11 08:56:42 INFO: ***** Start a BUSCO v5.4.3 analysis, current time: 08/11/2022 08:56:42 *****
+2022-08-11 08:56:42 INFO: Configuring BUSCO with local environment
+2022-08-11 08:56:42 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
+2022-08-11 08:56:42 INFO: Mode is genome
+2022-08-11 08:56:42 INFO: Downloading information on latest versions of BUSCO data...
+2022-08-11 08:56:54 INFO: Input file is /busco_wd/test_data/bacteria/genome.fna
+2022-08-11 08:56:54 INFO: No lineage specified. Running lineage auto selector.
-2022-07-15 15:18:00 INFO: ***** Starting Auto Select Lineage *****
+2022-08-11 08:56:54 INFO: ***** Starting Auto Select Lineage *****
This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
-2022-07-15 15:18:00 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/archaea_odb10.2021-02-23.tar.gz'
-2022-07-15 15:18:06 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb10.tar.gz'
-2022-07-15 15:18:07 INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
-2022-07-15 15:18:07 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:18:07
-2022-07-15 15:18:08 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:18:08 INFO: ***** Run Prodigal on input to predict and extract genes *****
-2022-07-15 15:18:08 INFO: Running Prodigal with genetic code 11 in single mode
-2022-07-15 15:18:08 INFO: Running 1 job(s) on prodigal, starting at 07/15/2022 15:18:08
-2022-07-15 15:18:10 INFO: [prodigal] 1 of 1 task(s) completed
-2022-07-15 15:18:10 INFO: Genetic code 11 selected as optimal
-2022-07-15 15:18:10 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:18:10 INFO: Running 194 job(s) on hmmsearch, starting at 07/15/2022 15:18:10
-2022-07-15 15:18:11 INFO: [hmmsearch] 20 of 194 task(s) completed
-2022-07-15 15:18:11 INFO: [hmmsearch] 39 of 194 task(s) completed
-2022-07-15 15:18:11 INFO: [hmmsearch] 59 of 194 task(s) completed
-2022-07-15 15:18:11 INFO: [hmmsearch] 78 of 194 task(s) completed
-2022-07-15 15:18:11 INFO: [hmmsearch] 97 of 194 task(s) completed
-2022-07-15 15:18:11 INFO: [hmmsearch] 117 of 194 task(s) completed
-2022-07-15 15:18:12 INFO: [hmmsearch] 136 of 194 task(s) completed
-2022-07-15 15:18:12 INFO: [hmmsearch] 156 of 194 task(s) completed
-2022-07-15 15:18:12 INFO: [hmmsearch] 156 of 194 task(s) completed
-2022-07-15 15:18:12 INFO: [hmmsearch] 175 of 194 task(s) completed
-2022-07-15 15:18:12 INFO: [hmmsearch] 194 of 194 task(s) completed
-2022-07-15 15:18:12 INFO: Results: C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194
+2022-08-11 08:56:54 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/archaea_odb10.2021-02-23.tar.gz'
+2022-08-11 08:57:00 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb10.tar.gz'
+2022-08-11 08:57:00 INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
+2022-08-11 08:57:00 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 08:57:00
+2022-08-11 08:57:02 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 08:57:02 INFO: ***** Run Prodigal on input to predict and extract genes *****
+2022-08-11 08:57:02 INFO: Running Prodigal with genetic code 11 in single mode
+2022-08-11 08:57:02 INFO: Running 1 job(s) on prodigal, starting at 08/11/2022 08:57:02
+2022-08-11 08:57:03 INFO: [prodigal] 1 of 1 task(s) completed
+2022-08-11 08:57:03 INFO: Genetic code 11 selected as optimal
+2022-08-11 08:57:03 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 08:57:03 INFO: Running 194 job(s) on hmmsearch, starting at 08/11/2022 08:57:03
+2022-08-11 08:57:04 INFO: [hmmsearch] 20 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 39 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 59 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 78 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 97 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 117 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 136 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 156 of 194 task(s) completed
+2022-08-11 08:57:04 INFO: [hmmsearch] 175 of 194 task(s) completed
+2022-08-11 08:57:05 INFO: [hmmsearch] 194 of 194 task(s) completed
+2022-08-11 08:57:05 INFO: Results: C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194
-2022-07-15 15:18:12 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz'
-2022-07-15 15:18:13 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/bacteria_odb10.tar.gz'
-2022-07-15 15:18:14 INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
-2022-07-15 15:18:14 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:18:14
-2022-07-15 15:18:15 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:18:15 INFO: ***** Run Prodigal on input to predict and extract genes *****
-2022-07-15 15:18:15 INFO: Genetic code 11 selected as optimal
-2022-07-15 15:18:15 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:18:15 INFO: Running 124 job(s) on hmmsearch, starting at 07/15/2022 15:18:15
-2022-07-15 15:18:16 INFO: [hmmsearch] 13 of 124 task(s) completed
-2022-07-15 15:18:16 INFO: [hmmsearch] 25 of 124 task(s) completed
-2022-07-15 15:18:16 INFO: [hmmsearch] 38 of 124 task(s) completed
-2022-07-15 15:18:16 INFO: [hmmsearch] 50 of 124 task(s) completed
-2022-07-15 15:18:16 INFO: [hmmsearch] 63 of 124 task(s) completed
-2022-07-15 15:18:16 INFO: [hmmsearch] 75 of 124 task(s) completed
-2022-07-15 15:18:17 INFO: [hmmsearch] 87 of 124 task(s) completed
-2022-07-15 15:18:17 INFO: [hmmsearch] 100 of 124 task(s) completed
-2022-07-15 15:18:17 INFO: [hmmsearch] 112 of 124 task(s) completed
-2022-07-15 15:18:17 INFO: [hmmsearch] 124 of 124 task(s) completed
-2022-07-15 15:18:17 INFO: Results: C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124
+2022-08-11 08:57:05 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz'
+2022-08-11 08:57:06 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/bacteria_odb10.tar.gz'
+2022-08-11 08:57:07 INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
+2022-08-11 08:57:07 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 08:57:07
+2022-08-11 08:57:08 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 08:57:08 INFO: ***** Run Prodigal on input to predict and extract genes *****
+2022-08-11 08:57:08 INFO: Genetic code 11 selected as optimal
+2022-08-11 08:57:08 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 08:57:08 INFO: Running 124 job(s) on hmmsearch, starting at 08/11/2022 08:57:08
+2022-08-11 08:57:09 INFO: [hmmsearch] 13 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 38 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 50 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 63 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 75 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 87 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 100 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 112 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: [hmmsearch] 124 of 124 task(s) completed
+2022-08-11 08:57:09 INFO: Results: C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124
-2022-07-15 15:18:17 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz'
-2022-07-15 15:18:20 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb10.tar.gz'
-2022-07-15 15:18:22 INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
-2022-07-15 15:18:22 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:18:22
-2022-07-15 15:18:23 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:18:26 INFO: Running 1 job(s) on metaeuk, starting at 07/15/2022 15:18:26
-2022-07-15 15:18:49 INFO: [metaeuk] 1 of 1 task(s) completed
-2022-07-15 15:18:49 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:18:49 INFO: Running 255 job(s) on hmmsearch, starting at 07/15/2022 15:18:49
-2022-07-15 15:18:50 INFO: [hmmsearch] 26 of 255 task(s) completed
-2022-07-15 15:18:50 INFO: [hmmsearch] 51 of 255 task(s) completed
-2022-07-15 15:18:50 INFO: [hmmsearch] 77 of 255 task(s) completed
-2022-07-15 15:18:50 INFO: [hmmsearch] 102 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 128 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 153 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 179 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 204 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 230 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 230 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: [hmmsearch] 255 of 255 task(s) completed
-2022-07-15 15:18:51 INFO: Results: C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255
+2022-08-11 08:57:09 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz'
+2022-08-11 08:57:13 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb10.tar.gz'
+2022-08-11 08:57:16 INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
+2022-08-11 08:57:16 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 08:57:16
+2022-08-11 08:57:17 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 08:57:20 INFO: Running 1 job(s) on metaeuk, starting at 08/11/2022 08:57:20
+2022-08-11 08:57:40 INFO: [metaeuk] 1 of 1 task(s) completed
+2022-08-11 08:57:40 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 08:57:40 INFO: Running 255 job(s) on hmmsearch, starting at 08/11/2022 08:57:40
+2022-08-11 08:57:40 INFO: [hmmsearch] 26 of 255 task(s) completed
+2022-08-11 08:57:40 INFO: [hmmsearch] 51 of 255 task(s) completed
+2022-08-11 08:57:40 INFO: [hmmsearch] 77 of 255 task(s) completed
+2022-08-11 08:57:40 INFO: [hmmsearch] 102 of 255 task(s) completed
+2022-08-11 08:57:40 INFO: [hmmsearch] 128 of 255 task(s) completed
+2022-08-11 08:57:41 INFO: [hmmsearch] 153 of 255 task(s) completed
+2022-08-11 08:57:41 INFO: [hmmsearch] 179 of 255 task(s) completed
+2022-08-11 08:57:41 INFO: [hmmsearch] 204 of 255 task(s) completed
+2022-08-11 08:57:41 INFO: [hmmsearch] 230 of 255 task(s) completed
+2022-08-11 08:57:41 INFO: [hmmsearch] 255 of 255 task(s) completed
+2022-08-11 08:57:41 INFO: Results: C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255
-2022-07-15 15:18:51 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
-2022-07-15 15:19:07 INFO: Running 1 job(s) on metaeuk, starting at 07/15/2022 15:19:07
-2022-07-15 15:19:37 INFO: [metaeuk] 1 of 1 task(s) completed
-2022-07-15 15:19:37 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:19:37 INFO: Running 252 job(s) on hmmsearch, starting at 07/15/2022 15:19:37
-2022-07-15 15:19:40 INFO: [hmmsearch] 51 of 252 task(s) completed
-2022-07-15 15:19:41 INFO: [hmmsearch] 76 of 252 task(s) completed
-2022-07-15 15:19:42 INFO: [hmmsearch] 101 of 252 task(s) completed
-2022-07-15 15:19:42 INFO: [hmmsearch] 126 of 252 task(s) completed
-2022-07-15 15:19:42 INFO: [hmmsearch] 152 of 252 task(s) completed
-2022-07-15 15:19:43 INFO: [hmmsearch] 177 of 252 task(s) completed
-2022-07-15 15:19:43 INFO: [hmmsearch] 202 of 252 task(s) completed
-2022-07-15 15:19:43 INFO: [hmmsearch] 227 of 252 task(s) completed
-2022-07-15 15:19:43 INFO: [hmmsearch] 252 of 252 task(s) completed
-2022-07-15 15:19:43 INFO: Validating exons and removing overlapping matches
-2022-07-15 15:19:43 INFO: Results: C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255
+2022-08-11 08:57:41 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
+2022-08-11 08:57:57 INFO: Running 1 job(s) on metaeuk, starting at 08/11/2022 08:57:57
+2022-08-11 08:58:24 INFO: [metaeuk] 1 of 1 task(s) completed
+2022-08-11 08:58:24 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 08:58:24 INFO: Running 252 job(s) on hmmsearch, starting at 08/11/2022 08:58:24
+2022-08-11 08:58:24 INFO: [hmmsearch] 26 of 252 task(s) completed
+2022-08-11 08:58:24 INFO: [hmmsearch] 51 of 252 task(s) completed
+2022-08-11 08:58:24 INFO: [hmmsearch] 76 of 252 task(s) completed
+2022-08-11 08:58:24 INFO: [hmmsearch] 101 of 252 task(s) completed
+2022-08-11 08:58:25 INFO: [hmmsearch] 152 of 252 task(s) completed
+2022-08-11 08:58:25 INFO: [hmmsearch] 177 of 252 task(s) completed
+2022-08-11 08:58:25 INFO: [hmmsearch] 202 of 252 task(s) completed
+2022-08-11 08:58:25 INFO: [hmmsearch] 252 of 252 task(s) completed
+2022-08-11 08:58:25 INFO: Validating exons and removing overlapping matches
+2022-08-11 08:58:25 INFO: Results: C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255
-2022-07-15 15:19:43 INFO: bacteria_odb10 selected
+2022-08-11 08:58:25 INFO: bacteria_odb10 selected
-2022-07-15 15:19:43 INFO: ***** Searching tree for chosen lineage to find best taxonomic match *****
+2022-08-11 08:58:25 INFO: ***** Searching tree for chosen lineage to find best taxonomic match *****
-2022-07-15 15:19:43 INFO: Extract markers...
-2022-07-15 15:19:43 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:19:43 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:19:43 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree.bacteria_odb10.2019-12-16.nwk.tar.gz'
-2022-07-15 15:19:49 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk.tar.gz'
-2022-07-15 15:19:49 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:19:55 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:19:55 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa.tar.gz'
-2022-07-15 15:20:02 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa.tar.gz'
-2022-07-15 15:20:03 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:20:08 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:20:08 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:20:14 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:20:14 INFO: Place the markers on the reference tree...
-2022-07-15 15:20:14 INFO: Running 1 job(s) on sepp, starting at 07/15/2022 15:20:14
-2022-07-15 15:21:01 INFO: [sepp] 1 of 1 task(s) completed
-2022-07-15 15:21:02 INFO: Not enough markers were placed on the tree (11). Root lineage bacteria is kept
-2022-07-15 15:21:02 INFO:
+2022-08-11 08:58:25 INFO: Extract markers...
+2022-08-11 08:58:25 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:25 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:25 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree.bacteria_odb10.2019-12-16.nwk.tar.gz'
+2022-08-11 08:58:31 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk.tar.gz'
+2022-08-11 08:58:31 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:37 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:37 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa.tar.gz'
+2022-08-11 08:58:44 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa.tar.gz'
+2022-08-11 08:58:45 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:50 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:50 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:56 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 08:58:56 INFO: Place the markers on the reference tree...
+2022-08-11 08:58:56 INFO: Running 1 job(s) on sepp, starting at 08/11/2022 08:58:56
+2022-08-11 08:59:51 INFO: [sepp] 1 of 1 task(s) completed
+2022-08-11 08:59:51 INFO: Not enough markers were placed on the tree (11). Root lineage bacteria is kept
+2022-08-11 08:59:51 INFO:
--------------------------------------------------
|Results from dataset bacteria_odb10 |
@@ -129,12 +125,12 @@
|97 Missing BUSCOs (M) |
|124 Total BUSCO groups searched |
--------------------------------------------------
-2022-07-15 15:21:02 INFO: BUSCO analysis done with WARNING(s). Total running time: 181 seconds
+2022-08-11 08:59:51 INFO: BUSCO analysis done with WARNING(s). Total running time: 177 seconds
***** Summary of warnings: *****
-2022-07-15 15:17:48 WARNING:busco.BuscoConfig Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
+2022-08-11 08:56:42 WARNING:busco.BuscoConfig Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
-2022-07-15 15:21:02 INFO: Results written in /busco_wd/test_bacteria
-2022-07-15 15:21:02 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
+2022-08-11 08:59:51 INFO: Results written in /busco_wd/test_bacteria
+2022-08-11 08:59:51 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
-2022-07-15 15:21:02 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
+2022-08-11 08:59:51 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
=====================================
test_data/eukaryota/expected_log.txt
=====================================
@@ -1,153 +1,154 @@
-2022-07-15 15:22:14 INFO: ***** Start a BUSCO v5.4.2 analysis, current time: 07/15/2022 15:22:14 *****
-2022-07-15 15:22:14 INFO: Configuring BUSCO with local environment
-2022-07-15 15:22:14 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
-2022-07-15 15:22:14 INFO: Mode is genome
-2022-07-15 15:22:14 INFO: Downloading information on latest versions of BUSCO data...
-2022-07-15 15:22:26 INFO: Input file is /busco_wd/test_data/eukaryota/genome.fna
-2022-07-15 15:22:26 INFO: No lineage specified. Running lineage auto selector.
+2022-08-11 09:03:07 INFO: ***** Start a BUSCO v5.4.3 analysis, current time: 08/11/2022 09:03:07 *****
+2022-08-11 09:03:07 INFO: Configuring BUSCO with local environment
+2022-08-11 09:03:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
+2022-08-11 09:03:07 INFO: Mode is genome
+2022-08-11 09:03:07 INFO: Downloading information on latest versions of BUSCO data...
+2022-08-11 09:03:19 INFO: Input file is /busco_wd/test_data/eukaryota/genome.fna
+2022-08-11 09:03:19 INFO: No lineage specified. Running lineage auto selector.
-2022-07-15 15:22:26 INFO: ***** Starting Auto Select Lineage *****
+2022-08-11 09:03:19 INFO: ***** Starting Auto Select Lineage *****
This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
-2022-07-15 15:22:26 INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
-2022-07-15 15:22:26 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:22:26
-2022-07-15 15:22:27 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:22:27 INFO: ***** Run Prodigal on input to predict and extract genes *****
-2022-07-15 15:22:27 INFO: Running Prodigal with genetic code 11 in single mode
-2022-07-15 15:22:27 INFO: Running 1 job(s) on prodigal, starting at 07/15/2022 15:22:27
-2022-07-15 15:22:28 INFO: [prodigal] 1 of 1 task(s) completed
-2022-07-15 15:22:28 INFO: Genetic code 11 selected as optimal
-2022-07-15 15:22:28 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:22:28 INFO: Running 194 job(s) on hmmsearch, starting at 07/15/2022 15:22:28
-2022-07-15 15:22:29 INFO: [hmmsearch] 20 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 39 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 59 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 78 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 97 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 117 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 136 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 156 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 175 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: [hmmsearch] 194 of 194 task(s) completed
-2022-07-15 15:22:29 INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.5%,M:98.5%,n:194
+2022-08-11 09:03:19 INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
+2022-08-11 09:03:19 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 09:03:19
+2022-08-11 09:03:20 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 09:03:20 INFO: ***** Run Prodigal on input to predict and extract genes *****
+2022-08-11 09:03:20 INFO: Running Prodigal with genetic code 11 in single mode
+2022-08-11 09:03:20 INFO: Running 1 job(s) on prodigal, starting at 08/11/2022 09:03:20
+2022-08-11 09:03:21 INFO: [prodigal] 1 of 1 task(s) completed
+2022-08-11 09:03:21 INFO: Genetic code 11 selected as optimal
+2022-08-11 09:03:21 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 09:03:21 INFO: Running 194 job(s) on hmmsearch, starting at 08/11/2022 09:03:21
+2022-08-11 09:03:22 INFO: [hmmsearch] 20 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 39 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 59 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 78 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 97 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 97 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 117 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 136 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 136 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 156 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 175 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: [hmmsearch] 194 of 194 task(s) completed
+2022-08-11 09:03:22 INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.5%,M:98.5%,n:194
-2022-07-15 15:22:30 INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
-2022-07-15 15:22:30 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:22:30
-2022-07-15 15:22:30 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:22:30 INFO: ***** Run Prodigal on input to predict and extract genes *****
-2022-07-15 15:22:30 INFO: Genetic code 11 selected as optimal
-2022-07-15 15:22:30 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:22:30 INFO: Running 124 job(s) on hmmsearch, starting at 07/15/2022 15:22:30
-2022-07-15 15:22:31 INFO: [hmmsearch] 13 of 124 task(s) completed
-2022-07-15 15:22:31 INFO: [hmmsearch] 25 of 124 task(s) completed
-2022-07-15 15:22:31 INFO: [hmmsearch] 38 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 50 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 63 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 75 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 87 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 100 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 112 of 124 task(s) completed
-2022-07-15 15:22:32 INFO: [hmmsearch] 124 of 124 task(s) completed
-2022-07-15 15:22:32 WARNING: BUSCO did not find any match. Make sure to check the log files if this is unexpected.
-2022-07-15 15:22:32 INFO: Results: C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124
+2022-08-11 09:03:22 INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
+2022-08-11 09:03:22 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 09:03:22
+2022-08-11 09:03:23 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 09:03:23 INFO: ***** Run Prodigal on input to predict and extract genes *****
+2022-08-11 09:03:23 INFO: Genetic code 11 selected as optimal
+2022-08-11 09:03:23 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 09:03:23 INFO: Running 124 job(s) on hmmsearch, starting at 08/11/2022 09:03:23
+2022-08-11 09:03:24 INFO: [hmmsearch] 13 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 25 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 25 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 50 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 63 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 75 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 87 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 100 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 112 of 124 task(s) completed
+2022-08-11 09:03:24 INFO: [hmmsearch] 124 of 124 task(s) completed
+2022-08-11 09:03:24 WARNING: BUSCO did not find any match. Make sure to check the log files if this is unexpected.
+2022-08-11 09:03:24 INFO: Results: C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124
-2022-07-15 15:22:32 INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
-2022-07-15 15:22:32 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:22:32
-2022-07-15 15:22:33 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:22:33 INFO: Running 1 job(s) on metaeuk, starting at 07/15/2022 15:22:33
-2022-07-15 15:22:54 INFO: [metaeuk] 1 of 1 task(s) completed
-2022-07-15 15:22:54 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:22:54 INFO: Running 255 job(s) on hmmsearch, starting at 07/15/2022 15:22:54
-2022-07-15 15:22:54 INFO: [hmmsearch] 26 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 77 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 102 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 128 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 153 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 179 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 204 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 230 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: [hmmsearch] 255 of 255 task(s) completed
-2022-07-15 15:22:55 INFO: Results: C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255
+2022-08-11 09:03:24 INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
+2022-08-11 09:03:24 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 09:03:24
+2022-08-11 09:03:25 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 09:03:25 INFO: Running 1 job(s) on metaeuk, starting at 08/11/2022 09:03:25
+2022-08-11 09:03:45 INFO: [metaeuk] 1 of 1 task(s) completed
+2022-08-11 09:03:45 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 09:03:45 INFO: Running 255 job(s) on hmmsearch, starting at 08/11/2022 09:03:45
+2022-08-11 09:03:46 INFO: [hmmsearch] 26 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 51 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 77 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 102 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 153 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 179 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 204 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 230 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: [hmmsearch] 255 of 255 task(s) completed
+2022-08-11 09:03:46 INFO: Results: C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255
-2022-07-15 15:22:55 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
-2022-07-15 15:23:10 INFO: Running 1 job(s) on metaeuk, starting at 07/15/2022 15:23:10
-2022-07-15 15:23:27 INFO: [metaeuk] 1 of 1 task(s) completed
-2022-07-15 15:23:27 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:23:27 INFO: Running 206 job(s) on hmmsearch, starting at 07/15/2022 15:23:27
-2022-07-15 15:23:28 INFO: [hmmsearch] 21 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 42 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 62 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 83 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 104 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 124 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 145 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 165 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 165 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 186 of 206 task(s) completed
-2022-07-15 15:23:28 INFO: [hmmsearch] 206 of 206 task(s) completed
-2022-07-15 15:23:29 INFO: Validating exons and removing overlapping matches
-2022-07-15 15:23:29 INFO: Results: C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255
+2022-08-11 09:03:46 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
+2022-08-11 09:04:01 INFO: Running 1 job(s) on metaeuk, starting at 08/11/2022 09:04:01
+2022-08-11 09:04:16 INFO: [metaeuk] 1 of 1 task(s) completed
+2022-08-11 09:04:16 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 09:04:16 INFO: Running 206 job(s) on hmmsearch, starting at 08/11/2022 09:04:16
+2022-08-11 09:04:17 INFO: [hmmsearch] 21 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 42 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 62 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 83 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 104 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 124 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 145 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 186 of 206 task(s) completed
+2022-08-11 09:04:17 INFO: [hmmsearch] 206 of 206 task(s) completed
+2022-08-11 09:04:18 INFO: Validating exons and removing overlapping matches
+2022-08-11 09:04:18 INFO: Results: C:19.2%[S:19.2%,D:0.0%],F:0.8%,M:80.0%,n:255
-2022-07-15 15:23:29 INFO: eukaryota_odb10 selected
+2022-08-11 09:04:18 INFO: eukaryota_odb10 selected
-2022-07-15 15:23:29 INFO: ***** Searching tree for chosen lineage to find best taxonomic match *****
+2022-08-11 09:04:18 INFO: ***** Searching tree for chosen lineage to find best taxonomic match *****
-2022-07-15 15:23:29 INFO: Extract markers...
-2022-07-15 15:23:29 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:23:29 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:23:29 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz'
-2022-07-15 15:23:35 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz'
-2022-07-15 15:23:35 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:23:41 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:23:41 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz'
-2022-07-15 15:23:48 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz'
-2022-07-15 15:23:48 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:23:54 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:23:54 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:24:00 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'
-2022-07-15 15:24:00 INFO: Place the markers on the reference tree...
-2022-07-15 15:24:00 INFO: Running 1 job(s) on sepp, starting at 07/15/2022 15:24:00
-2022-07-15 15:25:41 INFO: [sepp] 1 of 1 task(s) completed
-2022-07-15 15:25:41 INFO: Lineage saccharomycetes is selected, supported by 18 markers out of 19
-2022-07-15 15:25:41 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/saccharomycetes_odb10.2020-08-05.tar.gz'
-2022-07-15 15:25:43 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/saccharomycetes_odb10.tar.gz'
-2022-07-15 15:25:51 INFO: Running BUSCO using lineage dataset saccharomycetes_odb10 (eukaryota, 2020-08-05)
-2022-07-15 15:25:51 INFO: Running 1 job(s) on bbtools, starting at 07/15/2022 15:25:51
-2022-07-15 15:25:52 INFO: [bbtools] 1 of 1 task(s) completed
-2022-07-15 15:25:53 INFO: Running 1 job(s) on metaeuk, starting at 07/15/2022 15:25:53
-2022-07-15 15:25:58 INFO: [metaeuk] 1 of 1 task(s) completed
-2022-07-15 15:25:58 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:25:58 INFO: Running 2137 job(s) on hmmsearch, starting at 07/15/2022 15:25:58
-2022-07-15 15:26:00 INFO: [hmmsearch] 214 of 2137 task(s) completed
-2022-07-15 15:26:01 INFO: [hmmsearch] 428 of 2137 task(s) completed
-2022-07-15 15:26:02 INFO: [hmmsearch] 642 of 2137 task(s) completed
-2022-07-15 15:26:03 INFO: [hmmsearch] 855 of 2137 task(s) completed
-2022-07-15 15:26:04 INFO: [hmmsearch] 1069 of 2137 task(s) completed
-2022-07-15 15:26:05 INFO: [hmmsearch] 1283 of 2137 task(s) completed
-2022-07-15 15:26:06 INFO: [hmmsearch] 1496 of 2137 task(s) completed
-2022-07-15 15:26:07 INFO: [hmmsearch] 1710 of 2137 task(s) completed
-2022-07-15 15:26:08 INFO: [hmmsearch] 1924 of 2137 task(s) completed
-2022-07-15 15:26:10 INFO: [hmmsearch] 2137 of 2137 task(s) completed
-2022-07-15 15:26:12 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
-2022-07-15 15:26:17 INFO: Running 1 job(s) on metaeuk, starting at 07/15/2022 15:26:17
-2022-07-15 15:26:22 INFO: [metaeuk] 1 of 1 task(s) completed
-2022-07-15 15:26:23 INFO: ***** Run HMMER on gene sequences *****
-2022-07-15 15:26:23 INFO: Running 2093 job(s) on hmmsearch, starting at 07/15/2022 15:26:23
-2022-07-15 15:26:27 INFO: [hmmsearch] 210 of 2093 task(s) completed
-2022-07-15 15:26:31 INFO: [hmmsearch] 419 of 2093 task(s) completed
-2022-07-15 15:26:32 INFO: [hmmsearch] 628 of 2093 task(s) completed
-2022-07-15 15:26:33 INFO: [hmmsearch] 838 of 2093 task(s) completed
-2022-07-15 15:26:34 INFO: [hmmsearch] 1047 of 2093 task(s) completed
-2022-07-15 15:26:35 INFO: [hmmsearch] 1256 of 2093 task(s) completed
-2022-07-15 15:26:36 INFO: [hmmsearch] 1466 of 2093 task(s) completed
-2022-07-15 15:26:37 INFO: [hmmsearch] 1675 of 2093 task(s) completed
-2022-07-15 15:26:38 INFO: [hmmsearch] 1884 of 2093 task(s) completed
-2022-07-15 15:26:39 INFO: [hmmsearch] 2093 of 2093 task(s) completed
-2022-07-15 15:26:41 INFO: Validating exons and removing overlapping matches
-2022-07-15 15:26:41 INFO: Results: C:2.1%[S:2.1%,D:0.0%],F:0.0%,M:97.9%,n:2137
+2022-08-11 09:04:18 INFO: Extract markers...
+2022-08-11 09:04:18 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:18 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:18 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz'
+2022-08-11 09:04:24 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz'
+2022-08-11 09:04:24 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:30 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:30 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz'
+2022-08-11 09:04:37 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz'
+2022-08-11 09:04:37 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:42 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:42 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:48 INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'
+2022-08-11 09:04:48 INFO: Place the markers on the reference tree...
+2022-08-11 09:04:48 INFO: Running 1 job(s) on sepp, starting at 08/11/2022 09:04:48
+2022-08-11 09:06:54 INFO: [sepp] 1 of 1 task(s) completed
+2022-08-11 09:06:55 INFO: Lineage saccharomycetes is selected, supported by 18 markers out of 19
+2022-08-11 09:06:55 INFO: Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/saccharomycetes_odb10.2020-08-05.tar.gz'
+2022-08-11 09:06:56 INFO: Decompressing file '/busco_wd/busco_downloads/lineages/saccharomycetes_odb10.tar.gz'
+2022-08-11 09:07:06 INFO: Running BUSCO using lineage dataset saccharomycetes_odb10 (eukaryota, 2020-08-05)
+2022-08-11 09:07:06 INFO: Running 1 job(s) on bbtools, starting at 08/11/2022 09:07:06
+2022-08-11 09:07:06 INFO: [bbtools] 1 of 1 task(s) completed
+2022-08-11 09:07:07 INFO: Running 1 job(s) on metaeuk, starting at 08/11/2022 09:07:07
+2022-08-11 09:07:10 INFO: [metaeuk] 1 of 1 task(s) completed
+2022-08-11 09:07:10 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 09:07:10 INFO: Running 2137 job(s) on hmmsearch, starting at 08/11/2022 09:07:10
+2022-08-11 09:07:11 INFO: [hmmsearch] 214 of 2137 task(s) completed
+2022-08-11 09:07:12 INFO: [hmmsearch] 428 of 2137 task(s) completed
+2022-08-11 09:07:12 INFO: [hmmsearch] 642 of 2137 task(s) completed
+2022-08-11 09:07:12 INFO: [hmmsearch] 855 of 2137 task(s) completed
+2022-08-11 09:07:13 INFO: [hmmsearch] 1069 of 2137 task(s) completed
+2022-08-11 09:07:13 INFO: [hmmsearch] 1069 of 2137 task(s) completed
+2022-08-11 09:07:13 INFO: [hmmsearch] 1069 of 2137 task(s) completed
+2022-08-11 09:07:13 INFO: [hmmsearch] 1283 of 2137 task(s) completed
+2022-08-11 09:07:14 INFO: [hmmsearch] 1496 of 2137 task(s) completed
+2022-08-11 09:07:14 INFO: [hmmsearch] 1710 of 2137 task(s) completed
+2022-08-11 09:07:14 INFO: [hmmsearch] 1924 of 2137 task(s) completed
+2022-08-11 09:07:15 INFO: [hmmsearch] 2137 of 2137 task(s) completed
+2022-08-11 09:07:17 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...
+2022-08-11 09:07:22 INFO: Running 1 job(s) on metaeuk, starting at 08/11/2022 09:07:22
+2022-08-11 09:07:25 INFO: [metaeuk] 1 of 1 task(s) completed
+2022-08-11 09:07:26 INFO: ***** Run HMMER on gene sequences *****
+2022-08-11 09:07:26 INFO: Running 2093 job(s) on hmmsearch, starting at 08/11/2022 09:07:26
+2022-08-11 09:07:27 INFO: [hmmsearch] 419 of 2093 task(s) completed
+2022-08-11 09:07:27 INFO: [hmmsearch] 628 of 2093 task(s) completed
+2022-08-11 09:07:28 INFO: [hmmsearch] 838 of 2093 task(s) completed
+2022-08-11 09:07:29 INFO: [hmmsearch] 1047 of 2093 task(s) completed
+2022-08-11 09:07:29 INFO: [hmmsearch] 1256 of 2093 task(s) completed
+2022-08-11 09:07:29 INFO: [hmmsearch] 1466 of 2093 task(s) completed
+2022-08-11 09:07:30 INFO: [hmmsearch] 1675 of 2093 task(s) completed
+2022-08-11 09:07:30 INFO: [hmmsearch] 1884 of 2093 task(s) completed
+2022-08-11 09:07:31 INFO: [hmmsearch] 2093 of 2093 task(s) completed
+2022-08-11 09:07:33 INFO: Validating exons and removing overlapping matches
+2022-08-11 09:07:33 INFO: Results: C:2.1%[S:2.1%,D:0.0%],F:0.0%,M:97.9%,n:2137
-2022-07-15 15:26:41 INFO:
+2022-08-11 09:07:33 INFO:
--------------------------------------------------
|Results from generic domain eukaryota_odb10 |
@@ -172,13 +173,13 @@
|2091 Missing BUSCOs (M) |
|2137 Total BUSCO groups searched |
--------------------------------------------------
-2022-07-15 15:26:41 INFO: BUSCO analysis done with WARNING(s). Total running time: 255 seconds
+2022-08-11 09:07:33 INFO: BUSCO analysis done with WARNING(s). Total running time: 254 seconds
***** Summary of warnings: *****
-2022-07-15 15:22:14 WARNING:busco.BuscoConfig Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
-2022-07-15 15:22:32 WARNING:busco.busco_tools.hmmer BUSCO did not find any match. Make sure to check the log files if this is unexpected.
+2022-08-11 09:03:07 WARNING:busco.BuscoConfig Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
+2022-08-11 09:03:24 WARNING:busco.busco_tools.hmmer BUSCO did not find any match. Make sure to check the log files if this is unexpected.
-2022-07-15 15:26:41 INFO: Results written in /busco_wd/test_eukaryota
-2022-07-15 15:26:41 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
+2022-08-11 09:07:33 INFO: Results written in /busco_wd/test_eukaryota
+2022-08-11 09:07:33 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
-2022-07-15 15:26:41 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
+2022-08-11 09:07:33 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/402d6d9deece1f7eeb77ee5353cbf3a808be74fc...74b73f5ed8b709dd9aef137721f3cb33d730f9ef
--
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/402d6d9deece1f7eeb77ee5353cbf3a808be74fc...74b73f5ed8b709dd9aef137721f3cb33d730f9ef
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