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Hello! This is an automated update of the following workflow: workflows/genome_annotation/annotation-braker3. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

  • toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2

The workflow release number has been updated from 0.1 to 0.2.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 0
Failure 1
Skipped 0
Failed Tests
  • ❌ Genome_annotation_with_braker3.ga_0

    Problems:

    • Output with path /tmp/tmptp3iqjgn/Busco on dataset 1 GFF - Specific lineage__f5d3f9e5-c201-42ea-8b34-92d5d6f10951.gff3 different than expected
      Expected 5257+-0 lines in the output found 5256
      
    • Output with path /tmp/tmpioay4fnl/Busco on dataset 11 GFF - Specific lineage__31db2ac6-021e-4f32-91ea-3bc34ab64dcc.gff3 different than expected
      Expected 1+-0 lines in the output found 0
      

    Workflow invocation details

    • Invocation Messages

    • Steps
      • Step 1: BUSCO database:

        • step_state: scheduled
      • Step 2: Include BUSCO:

        • step_state: scheduled
      • Step 11: GFFRead:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmp8jp2rbkl/files/3/3/b/dataset_33bf0346-bbe8-40a0-8e8c-ca0cefb1c2c8.dat' genomeref.fa &&  gffread '/tmp/tmp8jp2rbkl/files/6/e/c/dataset_6ec2231e-eafd-4ab6-8f08-cc6eba1448d8.dat' -g genomeref.fa      -y pep.fa

            Exit Code:

            • 0

            Standard Error:

            • FASTA index file genomeref.fa.fai created.
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "d60b8b52d5fa11f0ae2b7ced8d3ca3a7"
              chr_replace None
              chromInfo "/tmp/tmp8jp2rbkl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              decode_url false
              expose false
              filtering None
              full_gff_attribute_preservation false
              gffs {"__current_case__": 0, "gff_fmt": "none"}
              maxintron None
              merging {"__current_case__": 0, "merge_sel": "none"}
              reference_genome {"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}
              region {"__current_case__": 0, "region_filter": "none"}
      • Step 12: OMArk:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5' --query '/tmp/tmp8jp2rbkl/files/8/7/e/dataset_87efe86e-5bec-467d-abdc-12018f6fa0b7.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5'      -o omark_galaxy

            Exit Code:

            • 0

            Standard Error:

            • ================================================================================
              
                 _____ _____ _____
                |     |     |  _  |_____ ___ ___
                |  |  | | | |     |     | -_|  _|
                |_____|_|_|_|__|__|_|_|_|___|_|   v2.1.0
              
                OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
                  
              ================================================================================
              
              Loading required libraries  [DONE]
              
              ================================================================================
              
              Running OMAmer on 44fe94d2209e, using:
               - database: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
               - query: /tmp/tmp8jp2rbkl/files/8/7/e/dataset_87efe86e-5bec-467d-abdc-12018f6fa0b7.dat
               - version: 2.1.0
              
              ================================================================================
              WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
              
              Loading data required for OMAmer search from database...
               - taxonomy information (0.9s) [DONE]
               - family information (0.6s) [DONE]
               - sub-family information (9.2s) [DONE]
               - family hierarchy (0.3s) [DONE]
               - k-mer index (6:39.6) [DONE]
               - family probability estimates (0.2s) [DONE]
               - sub-family probability estimates (1.0s) [DONE]
              
              Finished loading required data
              
              ================================================================================
              
              �[?25l
              Searching -  0 queries in 0s (0.0 queries/s) 
              Searching -  0 queries in 5s (0.0 queries/s) 
              Searching -  0 queries in 10s (0.0 queries/s) 
              Searching -  0 queries in 15s (0.0 queries/s) 
              Searching -  0 queries in 20s (0.0 queries/s) 
              Searching -  0 queries in 25s (0.0 queries/s) 
              Searching -  0 queries in 30s (0.0 queries/s) 
              Searching -  0 queries in 35s (0.0 queries/s) 
              Searching -  0 queries in 40s (0.0 queries/s) 
              Searching -  0 queries in 45s (0.0 queries/s) �[?25h�[J
              Searching -  1685 queries in 50.0s (33.69 queries/s) 
              
              ================================================================================
              
              OMAmer search complete:
               - results written to: output_omamer
               - total 466.26 seconds
               - search phase only 37.09 queries/s
              
              
              Note: family p-values are stated in negative log units.
              ================================================================================
              
              Thank you for using OMAmer. If you use OMAmer in your research, please cite:
              
              Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219
              
              
              OMAmer uses data from the OMA browser. Results can be interpreted further using:
               - OMA browser website (https://omabrowser.org)
               - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)
              
              ================================================================================
              WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
              NCBI database not present yet (first time used?)
              Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
              Done. Parsing...
              
              Inserting synonyms:          0 
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              Inserting taxid merges:      0 
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              Inserting taxids:           0 
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              Inserting taxids:       2045000 
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              Inserting taxids:       2055000 
              Inserting taxids:       2060000 
              Inserting taxids:       2065000 
              Inserting taxids:       2070000 
              Inserting taxids:       2075000 
              Inserting taxids:       2080000 
              Inserting taxids:       2085000 
              Inserting taxids:       2090000 
              Inserting taxids:       2095000 
              Inserting taxids:       2100000 
              Inserting taxids:       2105000 
              Inserting taxids:       2110000 
              Inserting taxids:       2115000 
              Inserting taxids:       2120000 
              Inserting taxids:       2125000 
              Inserting taxids:       2130000 
              Inserting taxids:       2135000 
              Inserting taxids:       2140000 
              Inserting taxids:       2145000 
              Inserting taxids:       2150000 
              Inserting taxids:       2155000 
              Inserting taxids:       2160000 
              Inserting taxids:       2165000 
              Inserting taxids:       2170000 
              Inserting taxids:       2175000 
              Inserting taxids:       2180000 
              Inserting taxids:       2185000 
              Inserting taxids:       2190000 
              Inserting taxids:       2195000 
              Inserting taxids:       2200000 
              Inserting taxids:       2205000 
              Inserting taxids:       2210000 
              Inserting taxids:       2215000 
              Inserting taxids:       2220000 
              Inserting taxids:       2225000 
              Inserting taxids:       2230000 
              Inserting taxids:       2235000 
              Inserting taxids:       2240000 
              Inserting taxids:       2245000 
              Inserting taxids:       2250000 
              Inserting taxids:       2255000 
              Inserting taxids:       2260000 
              Inserting taxids:       2265000 
              Inserting taxids:       2270000 
              Inserting taxids:       2275000 
              Inserting taxids:       2280000 
              Inserting taxids:       2285000 
              Inserting taxids:       2290000 
              Inserting taxids:       2295000 
              Inserting taxids:       2300000 
              Inserting taxids:       2305000 
              Inserting taxids:       2310000 
              Inserting taxids:       2315000 
              Inserting taxids:       2320000 
              Inserting taxids:       2325000 
              Inserting taxids:       2330000 
              Inserting taxids:       2335000 
              Inserting taxids:       2340000 
              Inserting taxids:       2345000 
              Inserting taxids:       2350000 
              Inserting taxids:       2355000 
              Inserting taxids:       2360000 
              Inserting taxids:       2365000 
              Inserting taxids:       2370000 
              Inserting taxids:       2375000 
              Inserting taxids:       2380000 
              Inserting taxids:       2385000 
              Inserting taxids:       2390000 
              Inserting taxids:       2395000 
              Inserting taxids:       2400000 
              Inserting taxids:       2405000 
              Inserting taxids:       2410000 
              Inserting taxids:       2415000 
              Inserting taxids:       2420000 
              Inserting taxids:       2425000 
              Inserting taxids:       2430000 
              Inserting taxids:       2435000 
              Inserting taxids:       2440000 
              Inserting taxids:       2445000 
              Inserting taxids:       2450000 
              Inserting taxids:       2455000 
              Inserting taxids:       2460000 
              Inserting taxids:       2465000 
              Inserting taxids:       2470000 
              Inserting taxids:       2475000 
              Inserting taxids:       2480000 
              Inserting taxids:       2485000 
              Inserting taxids:       2490000 
              Inserting taxids:       2495000 
              Inserting taxids:       2500000 
              Inserting taxids:       2505000 
              Inserting taxids:       2510000 
              Inserting taxids:       2515000 
              Inserting taxids:       2520000 
              Inserting taxids:       2525000 
              Inserting taxids:       2530000 
              Inserting taxids:       2535000 
              Inserting taxids:       2540000 
              Inserting taxids:       2545000 
              Inserting taxids:       2550000 
              Inserting taxids:       2555000 
              Inserting taxids:       2560000 
              Inserting taxids:       2565000 
              Inserting taxids:       2570000 
              Inserting taxids:       2575000 
              Inserting taxids:       2580000 
              Inserting taxids:       2585000 
              Inserting taxids:       2590000 
              Inserting taxids:       2595000 
              Inserting taxids:       2600000 
              Inserting taxids:       2605000 
              Inserting taxids:       2610000 
              Inserting taxids:       2615000 
              Inserting taxids:       2620000 
              Inserting taxids:       2625000 
              Inserting taxids:       2630000 
              Inserting taxids:       2635000 
              Inserting taxids:       2640000 
              Inserting taxids:       2645000 
              Inserting taxids:       2650000 
              Inserting taxids:       2655000 
              Inserting taxids:       2660000 
              Inserting taxids:       2665000 
              Inserting taxids:       2670000 
              Inserting taxids:       2675000 
              Inserting taxids:       2680000 
              Inserting taxids:       2685000 
              Inserting taxids:       2690000 
              Inserting taxids:       2695000 
              Inserting taxids:       2700000 
              Inserting taxids:       2705000 
              Inserting taxids:       2710000 WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
              
              WARNING:galaxy.model:Datatype class not found for extension 'sum'
              WARNING:galaxy.model:Datatype class not found for extension 'sum'
              WARNING:galaxy.model:Datatype class not found for extension 'sum'
              WARNING:galaxy.model:Datatype class not found for extension 'sum'
              WARNING:galaxy.model:Datatype class not found for extension 'sum'
              WARNING:galaxy.model:Datatype class not found for extension 'sum'
              

            Standard Output:

            • Loading node names...
              2711350 names loaded.
              425370 synonyms loaded.
              Loading nodes...
              2711350 nodes loaded.
              Linking nodes...
              Tree is loaded.
              Updating database: /tmp/tmp8jp2rbkl/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...
              
               0 generating entries... 
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              ..
              . 
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              Uploading to /tmp/tmp8jp2rbkl/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite
              
              
              
              
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "d60b8b52d5fa11f0ae2b7ced8d3ca3a7"
              chromInfo "/tmp/tmp8jp2rbkl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              database "LUCA-v2.0.0.h5"
              dbkey "?"
              input_iso None
              omark_mode false
              outputs "detail_sum"
              r None
              t None
      • Step 13: BUSCO on the predicted protein sequences:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmp8jp2rbkl/files/8/7/e/dataset_87efe86e-5bec-467d-abdc-12018f6fa0b7.dat' input.fa &&  busco --in 'input.fa' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path '/cvmfs/data.galaxyproject.org/byhand/busco/v5'  --lineage_dataset 'mucorales_odb10'   && cp busco_galaxy/run_*/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv && cp busco_galaxy/run_*/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv && mkdir BUSCO_summaries && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && cp BUSCO_summaries/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png  && echo "##gff-version 3" > busco_galaxy/busco_output.gff && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)

            Exit Code:

            • 0

            Standard Error:

            • 2025-12-10 19:54:39 ERROR:	
              Warning message:
              The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
              ℹ Please use the `linewidth` argument instead. 
              
              

            Standard Output:

            • 2025-12-10 19:51:14 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 12/10/2025 19:51:14 *****
              2025-12-10 19:51:14 INFO:	Configuring BUSCO with local environment
              2025-12-10 19:51:14 INFO:	Running proteins mode
              2025-12-10 19:51:14 INFO:	Input file is /tmp/tmp8jp2rbkl/job_working_directory/000/9/working/input.fa
              2025-12-10 19:51:14 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
              2025-12-10 19:51:14 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
              2025-12-10 19:51:14 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
              2025-12-10 19:51:14 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
              2025-12-10 19:51:14 INFO:	***** Run HMMER on gene sequences *****
              2025-12-10 19:51:14 INFO:	Running 2449 job(s) on hmmsearch, starting at 12/10/2025 19:51:14
              2025-12-10 19:51:40 INFO:	[hmmsearch]	245 of 2449 task(s) completed
              2025-12-10 19:52:01 INFO:	[hmmsearch]	490 of 2449 task(s) completed
              2025-12-10 19:52:18 INFO:	[hmmsearch]	735 of 2449 task(s) completed
              2025-12-10 19:52:39 INFO:	[hmmsearch]	980 of 2449 task(s) completed
              2025-12-10 19:52:57 INFO:	[hmmsearch]	1225 of 2449 task(s) completed
              2025-12-10 19:53:17 INFO:	[hmmsearch]	1470 of 2449 task(s) completed
              2025-12-10 19:53:36 INFO:	[hmmsearch]	1715 of 2449 task(s) completed
              2025-12-10 19:53:55 INFO:	[hmmsearch]	1960 of 2449 task(s) completed
              2025-12-10 19:54:13 INFO:	[hmmsearch]	2205 of 2449 task(s) completed
              2025-12-10 19:54:35 INFO:	[hmmsearch]	2449 of 2449 task(s) completed
              2025-12-10 19:54:36 INFO:	
              
                  ---------------------------------------------------
                  |Results from dataset mucorales_odb10              |
                  ---------------------------------------------------
                  |C:8.2%[S:7.8%,D:0.4%],F:0.7%,M:91.1%,n:2449       |
                  |201    Complete BUSCOs (C)                        |
                  |192    Complete and single-copy BUSCOs (S)        |
                  |9    Complete and duplicated BUSCOs (D)           |
                  |18    Fragmented BUSCOs (F)                       |
                  |2230    Missing BUSCOs (M)                        |
                  |2449    Total BUSCO groups searched               |
                  ---------------------------------------------------
              2025-12-10 19:54:36 INFO:	BUSCO analysis done with WARNING(s). Total running time: 202 seconds
              
              ***** Summary of warnings: *****
              2025-12-10 19:51:14 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
              2025-12-10 19:51:14 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
              2025-12-10 19:51:14 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins
              
              2025-12-10 19:54:36 INFO:	Results written in /tmp/tmp8jp2rbkl/job_working_directory/000/9/working/busco_galaxy
              2025-12-10 19:54:36 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
              
              2025-12-10 19:54:36 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
              2025-12-10 19:54:37 INFO:	****************** Start plot generation at 12/10/2025 19:54:37 ******************
              2025-12-10 19:54:37 INFO:	Load data ...
              2025-12-10 19:54:37 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
              2025-12-10 19:54:37 INFO:	Generate the R code ...
              2025-12-10 19:54:37 INFO:	Run the R code ...
              2025-12-10 19:54:39 INFO:	
              [1] "Plotting the figure ..."
              [1] "Done"
              
              2025-12-10 19:54:39 INFO:	Plot generation done. Total running time: 2.2236456871032715 seconds
              2025-12-10 19:54:39 INFO:	Results written in BUSCO_summaries/
              
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "d60b8b52d5fa11f0ae2b7ced8d3ca3a7"
              adv {"contig_break": "10", "evalue": "0.001", "limit": "3"}
              busco_mode {"__current_case__": 2, "mode": "prot"}
              cached_db "v5"
              chromInfo "/tmp/tmp8jp2rbkl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              lineage {"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}
              outputs ["short_summary", "image", "gff", "missing"]
              test None
      • Step 3: BUSCO lineage:

        • step_state: scheduled
      • Step 4: Soft masked Genome sequence:

        • step_state: scheduled
      • Step 5: Alignments from RNA-seq:

        • step_state: scheduled
      • Step 6: Protein sequences:

        • step_state: scheduled
      • Step 7: Fungus genome:

        • step_state: scheduled
      • Step 8: BUSCO on the genome sequences:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmp8jp2rbkl/files/3/3/b/dataset_33bf0346-bbe8-40a0-8e8c-ca0cefb1c2c8.dat' input.fa &&  busco --in 'input.fa' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path '/cvmfs/data.galaxyproject.org/byhand/busco/v5'  --lineage_dataset 'mucorales_odb10'  --miniprot  && cp busco_galaxy/run_*/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv && cp busco_galaxy/run_*/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv && mkdir BUSCO_summaries && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific && cp BUSCO_summaries/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png  && echo "##gff-version 3" > busco_galaxy/busco_output.gff && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)

            Exit Code:

            • 0

            Standard Error:

            • 2025-12-10 19:10:21 ERROR:	
              Warning message:
              The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
              ℹ Please use the `linewidth` argument instead. 
              
              

            Standard Output:

            • 2025-12-10 19:04:44 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 12/10/2025 19:04:44 *****
              2025-12-10 19:04:44 INFO:	Configuring BUSCO with local environment
              2025-12-10 19:04:44 INFO:	Running genome mode
              2025-12-10 19:04:45 INFO:	Input file is /tmp/tmp8jp2rbkl/job_working_directory/000/4/working/input.fa
              2025-12-10 19:04:45 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
              2025-12-10 19:04:45 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
              2025-12-10 19:04:45 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
              2025-12-10 19:04:45 INFO:	Running 1 job(s) on bbtools, starting at 12/10/2025 19:04:45
              2025-12-10 19:04:47 INFO:	[bbtools]	1 of 1 task(s) completed
              2025-12-10 19:04:47 INFO:	Running 1 job(s) on miniprot_index, starting at 12/10/2025 19:04:47
              2025-12-10 19:04:48 INFO:	[miniprot_index]	1 of 1 task(s) completed
              2025-12-10 19:04:48 WARNING:	Unable to remove compressed refseq file in dataset download
              2025-12-10 19:04:48 INFO:	Running 1 job(s) on miniprot_align, starting at 12/10/2025 19:04:48
              2025-12-10 19:07:39 INFO:	[miniprot_align]	1 of 1 task(s) completed
              2025-12-10 19:07:43 INFO:	***** Run HMMER on gene sequences *****
              2025-12-10 19:07:45 INFO:	Running 1269 job(s) on hmmsearch, starting at 12/10/2025 19:07:45
              2025-12-10 19:08:12 INFO:	[hmmsearch]	127 of 1269 task(s) completed
              2025-12-10 19:08:24 INFO:	[hmmsearch]	254 of 1269 task(s) completed
              2025-12-10 19:08:35 INFO:	[hmmsearch]	381 of 1269 task(s) completed
              2025-12-10 19:08:46 INFO:	[hmmsearch]	508 of 1269 task(s) completed
              2025-12-10 19:09:04 INFO:	[hmmsearch]	635 of 1269 task(s) completed
              2025-12-10 19:09:18 INFO:	[hmmsearch]	762 of 1269 task(s) completed
              2025-12-10 19:09:34 INFO:	[hmmsearch]	889 of 1269 task(s) completed
              2025-12-10 19:09:48 INFO:	[hmmsearch]	1016 of 1269 task(s) completed
              2025-12-10 19:10:03 INFO:	[hmmsearch]	1143 of 1269 task(s) completed
              2025-12-10 19:10:16 INFO:	[hmmsearch]	1269 of 1269 task(s) completed
              2025-12-10 19:10:16 INFO:	12 candidate overlapping regions found
              2025-12-10 19:10:16 INFO:	4006 exons in total
              2025-12-10 19:10:17 WARNING:	25 of 824 Complete matches (3.0%) contain internal stop codons in Miniprot gene predictions
              2025-12-10 19:10:17 INFO:	
              
                  -------------------------------------------------------------------------------------------
                  |Results from dataset mucorales_odb10                                                      |
                  -------------------------------------------------------------------------------------------
                  |C:33.6%[S:33.3%,D:0.3%],F:0.3%,M:66.0%,n:2449,E:3.0%                                      |
                  |824    Complete BUSCOs (C)    (of which 25 contain internal stop codons)                  |
                  |816    Complete and single-copy BUSCOs (S)                                                |
                  |8    Complete and duplicated BUSCOs (D)                                                   |
                  |8    Fragmented BUSCOs (F)                                                                |
                  |1617    Missing BUSCOs (M)                                                                |
                  |2449    Total BUSCO groups searched                                                       |
                  -------------------------------------------------------------------------------------------
              2025-12-10 19:10:17 INFO:	BUSCO analysis done with WARNING(s). Total running time: 332 seconds
              
              ***** Summary of warnings: *****
              2025-12-10 19:04:45 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_min
              2025-12-10 19:04:45 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_min
              2025-12-10 19:04:48 WARNING:busco.busco_tools.base	Unable to remove compressed refseq file in dataset download
              2025-12-10 19:10:17 WARNING:busco.busco_tools.hmmer	25 of 824 Complete matches (3.0%) contain internal stop codons in Miniprot gene predictions
              
              2025-12-10 19:10:17 INFO:	Results written in /tmp/tmp8jp2rbkl/job_working_directory/000/4/working/busco_galaxy
              2025-12-10 19:10:17 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html
              
              2025-12-10 19:10:17 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
              2025-12-10 19:10:18 INFO:	****************** Start plot generation at 12/10/2025 19:10:18 ******************
              2025-12-10 19:10:18 INFO:	Load data ...
              2025-12-10 19:10:18 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
              2025-12-10 19:10:18 INFO:	Generate the R code ...
              2025-12-10 19:10:18 INFO:	Run the R code ...
              2025-12-10 19:10:21 INFO:	
              [1] "Plotting the figure ..."
              [1] "Done"
              
              2025-12-10 19:10:21 INFO:	Plot generation done. Total running time: 2.44899582862854 seconds
              2025-12-10 19:10:21 INFO:	Results written in BUSCO_summaries/
              
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "d60b8b52d5fa11f0ae2b7ced8d3ca3a7"
              adv {"contig_break": "10", "evalue": "0.001", "limit": "3"}
              busco_mode {"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}
              cached_db "v5"
              chromInfo "/tmp/tmp8jp2rbkl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              lineage {"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}
              outputs ["short_summary", "image", "gff", "missing"]
              test None
      • Step 9: Braker3:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&   braker.pl --genome '/tmp/tmp8jp2rbkl/files/3/3/b/dataset_33bf0346-bbe8-40a0-8e8c-ca0cefb1c2c8.dat'   --bam /tmp/tmp8jp2rbkl/files/2/d/7/dataset_2d7c0480-99a0-4647-8160-b050d2921f3e.dat  --prot_seq /tmp/tmp8jp2rbkl/files/f/e/e/dataset_feebeb8e-1ae2-4fb1-8cac-64b16a88d985.dat   --gff3     --rounds 5          --alternatives-from-evidence=true    --gc_probability 0.001 --downsampling_lambda 2   --threads  ${GALAXY_SLOTS:-2} --useexisting

            Exit Code:

            • 0

            Standard Error:

            • #*********
              # WARNING: Detected whitespace in fasta header of file /tmp/tmp8jp2rbkl/files/f/e/e/dataset_feebeb8e-1ae2-4fb1-8cac-64b16a88d985.dat. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
              #*********
              #*********
              # WARNING: Detected | in fasta header of file /tmp/tmp8jp2rbkl/files/f/e/e/dataset_feebeb8e-1ae2-4fb1-8cac-64b16a88d985.dat. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
              #*********
              

            Standard Output:

            • # Wed Dec 10 19:05:53 2025:Both protein and RNA-Seq data in input detected. BRAKER will be executed in ETP mode (BRAKER3).
              #*********
              # Wed Dec 10 19:05:53 2025: Log information is stored in file /tmp/tmp8jp2rbkl/job_working_directory/000/5/working/braker/braker.log
              #*********
              # WARNING: Number of reliable training genes is low (74). Recommended are at least 600 genes
              #*********
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "d60b8b52d5fa11f0ae2b7ced8d3ca3a7"
              advanced {"alternatives_from_evidence": true, "eval": null, "eval_pseudo": null, "filterOutShort": false}
              augustus {"AUGUSTUS_ab_initio": false, "crf": false, "keepCrf": false, "rounds": "5"}
              chromInfo "/tmp/tmp8jp2rbkl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              dev {"downsampling_lambda": "2", "gc_probability": "0.001", "gm_max_intergenic": null, "min_contig": null, "splice_sites": null}
              evidences {"bam": {"values": [{"id": 2, "src": "hda"}]}, "prot_seq": {"values": [{"id": 3, "src": "hda"}]}}
              genemark {"fungus": false}
              output_format "gff3"
              softmasking true
              species None
      • Step 10: JBrowse instance with the BRAKER3 annotation track:

        • step_state: scheduled

        • Jobs
          • Job 1:

            • Job state is ok

            Command Line:

            • mkdir -p /tmp/tmp8jp2rbkl/job_working_directory/000/6/outputs/dataset_06026569-291c-4c06-8949-847e0a2370c6_files &&  cp /tmp/tmp8jp2rbkl/job_working_directory/000/6/configs/tmpn766i0v_ /tmp/tmp8jp2rbkl/job_working_directory/000/6/outputs/dataset_06026569-291c-4c06-8949-847e0a2370c6_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp8jp2rbkl/job_working_directory/000/6/outputs/dataset_06026569-291c-4c06-8949-847e0a2370c6_files /tmp/tmp8jp2rbkl/job_working_directory/000/6/configs/tmpn766i0v_ &&  cp /tmp/tmp8jp2rbkl/job_working_directory/000/6/outputs/dataset_06026569-291c-4c06-8949-847e0a2370c6_files/index.html /tmp/tmp8jp2rbkl/job_working_directory/000/6/outputs/dataset_06026569-291c-4c06-8949-847e0a2370c6.dat;

            Exit Code:

            • 0

            Standard Error:

            • INFO:jbrowse:Processing Braker3 Annotation / BRAKER3 on dataset 1-3: GFF Annotation
              WARNING: No feature names found for indexing, only reference sequence names will be indexed.
              

            Traceback:

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fasta"
              __workflow_invocation_uuid__ "d60b8b52d5fa11f0ae2b7ced8d3ca3a7"
              action {"__current_case__": 0, "action_select": "create"}
              chromInfo "/tmp/tmp8jp2rbkl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              gencode "1"
              jbgen {"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}
              plugins {"BlastView": true, "ComboTrackSelector": false, "GCContent": false}
              reference_genome {"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}
              standalone "minimal"
              track_groups [{"__index__": 0, "category": "Braker3 Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 9, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_on"}}]}]
              uglyTestingHack ""
    • Other invocation details
      • history_id

        • 4e95b4cc524d2933
      • history_state

        • ok
      • invocation_id

        • 4e95b4cc524d2933
      • invocation_state

        • scheduled
      • workflow_id

        • 4e95b4cc524d2933

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