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Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.
By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/bgruening/hifiasm/hifiasm/0.19.9+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
The workflow release number has been updated from 0.2.2 to 0.2.3.
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.
Output with path /tmp/tmpi5uqwd70/Hifiasm Primary assembly__824a6743-a59d-4a06-b029-d834bbc4a4f1 different than expected
Expected 170+-0 lines in the output found 168
Output with path /tmp/tmpbj1619ml/Hifiasm Alternate assembly__073d3996-2586-4d46-8627-a5128f5306b4 different than expected
Expected 2+-0 lines in the output found 6
Output with path /tmp/tmpnvjb3c00/gfastats on data 28 stats__299744a3-fcd5-4977-97ec-eedb63de8bd0 different than expected
Expected line '# scaffolds 1' in output ('Expected genome size 2,288,021
# scaffolds 3
Total scaffold length 34,014
Average scaffold length 11,338.00
Scaffold N50 11,612
Scaffold auN 11,441.29
Scaffold L50 2
Scaffold NG50 0
Scaffold auNG 170.09
Scaffold LG50 0
Largest scaffold 12,505
Smallest scaffold 9,897
# contigs 3
Total contig length 34,014
Average contig length 11,338.00
Contig N50 11,612
Contig auN 11,441.29
Contig L50 2
Contig NG50 0
Contig auNG 170.09
Contig LG50 0
Largest contig 12,505
Smallest contig 9,897
# gaps in scaffolds 0
Total gap length in scaffolds 0
Average gap length in scaffolds 0.00
Gap N50 in scaffolds 0
Gap auN in scaffolds 0.00
Gap L50 in scaffolds 0
Largest gap in scaffolds 0
Smallest gap in scaffolds 0
Base composition (A:C:G:T) 9,774:7,208:7,720:9,312
GC content % 43.89
# soft-masked bases 0
# segments 3
Total segment length 34,014
Average segment length 11,338.00
# gaps 0
# paths 3
# edges 4
Average degree 1.33
# connected components 1
Largest connected component length 34,014
# dead ends 3
# disconnected components 0
Total length disconnected components 0
# separated components 1
# bubbles 0
# circular segments 0
# circular paths 0
Scaffold N10 12,505
Scaffold N20 12,505
Scaffold N30 12,505
Scaffold N40 11,612
Scaffold N50 11,612
Scaffold N60 11,612
Scaffold N70 11,612
Scaffold N80 9,897
Scaffold N90 9,897
Scaffold N100 9,897
Scaffold L10 1
Scaffold L20 1
Scaffold L30 1
Scaffold L40 2
Scaffold L50 2
Scaffold L60 2
Scaffold L70 2
Scaffold L80 3
Scaffold L90 3
Scaffold L100 3
Scaffold NG10 0
Scaffold NG20 0
Scaffold NG30 0
Scaffold NG40 0
Scaffold NG50 0
Scaffold NG60 0
Scaffold NG70 0
Scaffold NG80 0
Scaffold NG90 0
Scaffold NG100 0
Scaffold LG10 0
Scaffold LG20 0
Scaffold LG30 0
Scaffold LG40 0
Scaffold LG50 0
Scaffold LG60 0
Scaffold LG70 0
Scaffold LG80 0
Scaffold LG90 0
Scaffold LG100 0
Contig N10 12,505
Contig N20 12,505
Contig N30 12,505
Contig N40 11,612
Contig N50 11,612
Contig N60 11,612
Contig N70 11,612
Contig N80 9,897
Contig N90 9,897
Contig N100 9,897
Contig L10 1
Contig L20 1
Contig L30 1
Contig L40 2
Contig L50 2
Contig L60 2
Contig L70 2
Contig L80 3
Contig L90 3
Contig L100 3
Contig NG10 0
Contig NG20 0
Contig NG30 0
Contig NG40 0
Contig NG50 0
Contig NG60 0
Contig NG70 0
Contig NG80 0
Contig NG90 0
Contig NG100 0
Contig LG10 0
Contig LG20 0
Contig LG30 0
Contig LG40 0
Contig LG50 0
Contig LG60 0
Contig LG70 0
Contig LG80 0
Contig LG90 0
Contig LG100 0
Gap N10 0
Gap N20 0
Gap N30 0
Gap N40 0
Gap N50 0
Gap N60 0
Gap N70 0
Gap N80 0
Gap N90 0
Gap N100 0
Gap L10 0
Gap L20 0
Gap L30 0
Gap L40 0
Gap L50 0
Gap L60 0
Gap L70 0
Gap L80 0
Gap L90 0
Gap L100 0
')
Output with path /tmp/tmpxoi27t97/gfastats on data 27 stats__b28c56cd-ab70-40e0-ba0c-0bd5c65b677a different than expected
Expected line '# scaffolds 85' in output ('Expected genome size 2,288,021
# scaffolds 84
Total scaffold length 2,052,441
Average scaffold length 24,433.82
Scaffold N50 22,011
Scaffold auN 34,199.59
Scaffold L50 31
Scaffold NG50 20,895
Scaffold auNG 30,678.32
Scaffold LG50 36
Largest scaffold 132,684
Smallest scaffold 15,406
# contigs 84
Total contig length 2,052,441
Average contig length 24,433.82
Contig N50 22,011
Contig auN 34,199.59
Contig L50 31
Contig NG50 20,895
Contig auNG 30,678.32
Contig LG50 36
Largest contig 132,684
Smallest contig 15,406
# gaps in scaffolds 0
Total gap length in scaffolds 0
Average gap length in scaffolds 0.00
Gap N50 in scaffolds 0
Gap auN in scaffolds 0.00
Gap L50 in scaffolds 0
Largest gap in scaffolds 0
Smallest gap in scaffolds 0
Base composition (A:C:G:T) 627,800:397,884:399,253:627,504
GC content % 38.84
# soft-masked bases 0
# segments 84
Total segment length 2,052,441
Average segment length 24,433.82
# gaps 0
# paths 84
# edges 8
Average degree 0.10
# connected components 2
Largest connected component length 96,664
# dead ends 162
# disconnected components 78
Total length disconnected components 1,895,760
# separated components 80
# bubbles 0
# circular segments 0
# circular paths 0
Scaffold N10 93,875
Scaffold N20 38,474
Scaffold N30 26,760
Scaffold N40 24,256
Scaffold N50 22,011
Scaffold N60 20,526
Scaffold N70 19,727
Scaffold N80 19,045
Scaffold N90 17,730
Scaffold N100 15,406
Scaffold L10 2
Scaffold L20 7
Scaffold L30 14
Scaffold L40 22
Scaffold L50 31
Scaffold L60 40
Scaffold L70 51
Scaffold L80 61
Scaffold L90 72
Scaffold L100 84
Scaffold NG10 46,449
Scaffold NG20 31,085
Scaffold NG30 25,225
Scaffold NG40 23,513
Scaffold NG50 20,895
Scaffold NG60 19,871
Scaffold NG70 19,102
Scaffold NG80 17,885
Scaffold NG90 0
Scaffold NG100 0
Scaffold LG10 3
Scaffold LG20 8
Scaffold LG30 16
Scaffold LG40 26
Scaffold LG50 36
Scaffold LG60 47
Scaffold LG70 59
Scaffold LG80 71
Scaffold LG90 0
Scaffold LG100 0
Contig N10 93,875
Contig N20 38,474
Contig N30 26,760
Contig N40 24,256
Contig N50 22,011
Contig N60 20,526
Contig N70 19,727
Contig N80 19,045
Contig N90 17,730
Contig N100 15,406
Contig L10 2
Contig L20 7
Contig L30 14
Contig L40 22
Contig L50 31
Contig L60 40
Contig L70 51
Contig L80 61
Contig L90 72
Contig L100 84
Contig NG10 46,449
Contig NG20 31,085
Contig NG30 25,225
Contig NG40 23,513
Contig NG50 20,895
Contig NG60 19,871
Contig NG70 19,102
Contig NG80 17,885
Contig NG90 0
Contig NG100 0
Contig LG10 3
Contig LG20 8
Contig LG30 16
Contig LG40 26
Contig LG50 36
Contig LG60 47
Contig LG70 59
Contig LG80 71
Contig LG90 0
Contig LG100 0
Gap N10 0
Gap N20 0
Gap N30 0
Gap N40 0
Gap N50 0
Gap N60 0
Gap N70 0
Gap N80 0
Gap N90 0
Gap N100 0
Gap L10 0
Gap L20 0
Gap L30 0
Gap L40 0
Gap L50 0
Gap L60 0
Gap L70 0
Gap L80 0
Gap L90 0
Gap L100 0
')
2024-12-09 04:56:02 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:
2024-12-09 04:34:57 INFO: ***** Start a BUSCO v5.8.0 analysis, current time: 12/09/2024 04:34:57 *****2024-12-09 04:34:57 INFO: Configuring BUSCO with local environment2024-12-09 04:34:57 INFO: Running genome mode2024-12-09 04:35:01 INFO: Input file is /tmp/tmpa8tjyvt3/files/8/2/4/dataset_824a6743-a59d-4a06-b029-d834bbc4a4f1.dat2024-12-09 04:35:01 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met2024-12-09 04:35:01 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met2024-12-09 04:35:02 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)2024-12-09 04:35:02 INFO: Running 1 job(s) on bbtools, starting at 12/09/2024 04:35:022024-12-09 04:35:03 INFO: [bbtools] 1 of 1 task(s) completed2024-12-09 04:35:03 INFO: Running 1 job(s) on metaeuk, starting at 12/09/2024 04:35:032024-12-09 04:40:02 INFO: [metaeuk] 1 of 1 task(s) completed2024-12-09 04:40:02 INFO: ***** Run HMMER on gene sequences *****2024-12-09 04:40:02 INFO: Running 3354 job(s) on hmmsearch, starting at 12/09/2024 04:40:022024-12-09 04:40:40 INFO: [hmmsearch] 336 of 3354 task(s) completed2024-12-09 04:41:15 INFO: [hmmsearch] 671 of 3354 task(s) completed2024-12-09 04:41:48 INFO: [hmmsearch] 1007 of 3354 task(s) completed2024-12-09 04:42:22 INFO: [hmmsearch] 1342 of 3354 task(s) completed2024-12-09 04:42:57 INFO: [hmmsearch] 1677 of 3354 task(s) completed2024-12-09 04:43:29 INFO: [hmmsearch] 2013 of 3354 task(s) completed2024-12-09 04:44:01 INFO: [hmmsearch] 2348 of 3354 task(s) completed2024-12-09 04:44:32 INFO: [hmmsearch] 2684 of 3354 task(s) completed2024-12-09 04:45:05 INFO: [hmmsearch] 3019 of 3354 task(s) completed2024-12-09 04:45:44 INFO: [hmmsearch] 3354 of 3354 task(s) completed2024-12-09 04:45:45 INFO: 59 exons in total2024-12-09 04:45:45 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...2024-12-09 04:47:32 INFO: Running 1 job(s) on metaeuk, starting at 12/09/2024 04:47:322024-12-09 04:55:23 INFO: [metaeuk] 1 of 1 task(s) completed2024-12-09 04:55:23 INFO: ***** Run HMMER on gene sequences *****2024-12-09 04:55:23 INFO: Running 3314 job(s) on hmmsearch, starting at 12/09/2024 04:55:232024-12-09 04:55:27 INFO: [hmmsearch] 332 of 3314 task(s) completed2024-12-09 04:55:31 INFO: [hmmsearch] 663 of 3314 task(s) completed2024-12-09 04:55:34 INFO: [hmmsearch] 995 of 3314 task(s) completed2024-12-09 04:55:37 INFO: [hmmsearch] 1326 of 3314 task(s) completed2024-12-09 04:55:41 INFO: [hmmsearch] 1657 of 3314 task(s) completed2024-12-09 04:55:44 INFO: [hmmsearch] 1989 of 3314 task(s) completed2024-12-09 04:55:48 INFO: [hmmsearch] 2320 of 3314 task(s) completed2024-12-09 04:55:52 INFO: [hmmsearch] 2652 of 3314 task(s) completed2024-12-09 04:55:55 INFO: [hmmsearch] 2983 of 3314 task(s) completed2024-12-09 04:55:58 INFO: [hmmsearch] 3314 of 3314 task(s) completed2024-12-09 04:55:59 INFO: 4 candidate overlapping regions found2024-12-09 04:55:59 INFO: 65 exons in total2024-12-09 04:55:59 INFO: Results: C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354 2024-12-09 04:55:59 INFO: --------------------------------------------------- |Results from dataset vertebrata_odb10 | --------------------------------------------------- |C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354 | |40 Complete BUSCOs (C) | |39 Complete and single-copy BUSCOs (S) | |1 Complete and duplicated BUSCOs (D) | |15 Fragmented BUSCOs (F) | |3299 Missing BUSCOs (M) | |3354 Total BUSCO groups searched | ---------------------------------------------------2024-12-09 04:55:59 INFO: BUSCO analysis done with WARNING(s). Total running time: 1258 seconds***** Summary of warnings: *****2024-12-09 04:35:01 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met2024-12-09 04:35:01 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met2024-12-09 04:55:59 INFO: Results written in /tmp/tmpa8tjyvt3/job_working_directory/000/27/working/busco_galaxy2024-12-09 04:55:59 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html2024-12-09 04:55:59 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCOtotal 140drwxr-xr-x 5 1001 118 4096 Dec 9 04:35 busco_sequences-rw-r--r-- 1 1001 118 76855 Dec 9 04:55 full_table.tsvdrwxr-xr-x 4 1001 118 4096 Dec 9 04:45 hmmer_outputdrwxr-xr-x 4 1001 118 4096 Dec 9 04:55 metaeuk_output-rw-r--r-- 1 1001 118 42328 Dec 9 04:55 missing_busco_list.tsv-rw-r--r-- 1 1001 118 2953 Dec 9 04:55 short_summary.json-rw-r--r-- 1 1001 118 969 Dec 9 04:55 short_summary.txt2024-12-09 04:56:00 INFO: ****************** Start plot generation at 12/09/2024 04:56:00 ******************2024-12-09 04:56:00 INFO: Load data ...2024-12-09 04:56:00 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully2024-12-09 04:56:00 INFO: Generate the R code ...2024-12-09 04:56:00 INFO: Run the R code ...2024-12-09 04:56:02 INFO: [1] "Plotting the figure ..."[1] "Done"2024-12-09 04:56:02 INFO: Plot generation done. Total running time: 2.008241891860962 seconds2024-12-09 04:56:02 INFO: Results written in BUSCO_summaries/
c3/2052441c2/1000000c3/1000000Computing 3 new columns with instructions ['c3/2052441;;', 'c2/1000000;;', 'c3/1000000;;']Computed new column values for 100.00% of 84 lines written.
c3/34014c2/1000000c3/1000000Computing 3 new columns with instructions ['c3/34014;;', 'c2/1000000;;', 'c3/1000000;;']Computed new column values for 100.00% of 3 lines written.
Warning message:In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honoredWarning message:package ‘ggplot2’ was built under R version 4.1.3 Warning message:Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.ℹ Please use `linewidth` instead.
Warning message:In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honoredWarning message:package ‘ggplot2’ was built under R version 4.1.3 Warning message:Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.ℹ Please use `linewidth` instead.
gxydevbot
changed the title
Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.2.2 to 0.2.3
Updating workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3 from 0.2.2 to 0.2.3
Dec 16, 2024
Output with path /tmp/tmprqugwc6u/Hifiasm Primary assembly__3c5f52df-9e1b-4009-ba59-9112e1b6d028 different than expected
Expected 170+-0 lines in the output found 168
Output with path /tmp/tmpnw2l4u6b/Hifiasm Alternate assembly__c76b7a37-9513-4ac1-8705-88621404f718 different than expected
Expected 2+-0 lines in the output found 6
Output with path /tmp/tmp3y1ih0b3/gfastats on data 28 stats__f555913d-19c0-4e07-8cbe-b5adbdbd7344 different than expected
Expected line '# scaffolds 1' in output ('Expected genome size 2,288,021
# scaffolds 3
Total scaffold length 34,014
Average scaffold length 11,338.00
Scaffold N50 11,612
Scaffold auN 11,441.29
Scaffold L50 2
Scaffold NG50 0
Scaffold auNG 170.09
Scaffold LG50 0
Largest scaffold 12,505
Smallest scaffold 9,897
# contigs 3
Total contig length 34,014
Average contig length 11,338.00
Contig N50 11,612
Contig auN 11,441.29
Contig L50 2
Contig NG50 0
Contig auNG 170.09
Contig LG50 0
Largest contig 12,505
Smallest contig 9,897
# gaps in scaffolds 0
Total gap length in scaffolds 0
Average gap length in scaffolds 0.00
Gap N50 in scaffolds 0
Gap auN in scaffolds 0.00
Gap L50 in scaffolds 0
Largest gap in scaffolds 0
Smallest gap in scaffolds 0
Base composition (A:C:G:T) 9,774:7,208:7,720:9,312
GC content % 43.89
# soft-masked bases 0
# segments 3
Total segment length 34,014
Average segment length 11,338.00
# gaps 0
# paths 3
# edges 4
Average degree 1.33
# connected components 1
Largest connected component length 34,014
# dead ends 3
# disconnected components 0
Total length disconnected components 0
# separated components 1
# bubbles 0
# circular segments 0
# circular paths 0
Scaffold N10 12,505
Scaffold N20 12,505
Scaffold N30 12,505
Scaffold N40 11,612
Scaffold N50 11,612
Scaffold N60 11,612
Scaffold N70 11,612
Scaffold N80 9,897
Scaffold N90 9,897
Scaffold N100 9,897
Scaffold L10 1
Scaffold L20 1
Scaffold L30 1
Scaffold L40 2
Scaffold L50 2
Scaffold L60 2
Scaffold L70 2
Scaffold L80 3
Scaffold L90 3
Scaffold L100 3
Scaffold NG10 0
Scaffold NG20 0
Scaffold NG30 0
Scaffold NG40 0
Scaffold NG50 0
Scaffold NG60 0
Scaffold NG70 0
Scaffold NG80 0
Scaffold NG90 0
Scaffold NG100 0
Scaffold LG10 0
Scaffold LG20 0
Scaffold LG30 0
Scaffold LG40 0
Scaffold LG50 0
Scaffold LG60 0
Scaffold LG70 0
Scaffold LG80 0
Scaffold LG90 0
Scaffold LG100 0
Contig N10 12,505
Contig N20 12,505
Contig N30 12,505
Contig N40 11,612
Contig N50 11,612
Contig N60 11,612
Contig N70 11,612
Contig N80 9,897
Contig N90 9,897
Contig N100 9,897
Contig L10 1
Contig L20 1
Contig L30 1
Contig L40 2
Contig L50 2
Contig L60 2
Contig L70 2
Contig L80 3
Contig L90 3
Contig L100 3
Contig NG10 0
Contig NG20 0
Contig NG30 0
Contig NG40 0
Contig NG50 0
Contig NG60 0
Contig NG70 0
Contig NG80 0
Contig NG90 0
Contig NG100 0
Contig LG10 0
Contig LG20 0
Contig LG30 0
Contig LG40 0
Contig LG50 0
Contig LG60 0
Contig LG70 0
Contig LG80 0
Contig LG90 0
Contig LG100 0
Gap N10 0
Gap N20 0
Gap N30 0
Gap N40 0
Gap N50 0
Gap N60 0
Gap N70 0
Gap N80 0
Gap N90 0
Gap N100 0
Gap L10 0
Gap L20 0
Gap L30 0
Gap L40 0
Gap L50 0
Gap L60 0
Gap L70 0
Gap L80 0
Gap L90 0
Gap L100 0
')
Output with path /tmp/tmpdyqzbyyb/gfastats on data 27 stats__b84ee980-3d44-47a4-8fcf-0d5b46205402 different than expected
Expected line '# scaffolds 85' in output ('Expected genome size 2,288,021
# scaffolds 84
Total scaffold length 2,052,441
Average scaffold length 24,433.82
Scaffold N50 22,011
Scaffold auN 34,199.59
Scaffold L50 31
Scaffold NG50 20,895
Scaffold auNG 30,678.32
Scaffold LG50 36
Largest scaffold 132,684
Smallest scaffold 15,406
# contigs 84
Total contig length 2,052,441
Average contig length 24,433.82
Contig N50 22,011
Contig auN 34,199.59
Contig L50 31
Contig NG50 20,895
Contig auNG 30,678.32
Contig LG50 36
Largest contig 132,684
Smallest contig 15,406
# gaps in scaffolds 0
Total gap length in scaffolds 0
Average gap length in scaffolds 0.00
Gap N50 in scaffolds 0
Gap auN in scaffolds 0.00
Gap L50 in scaffolds 0
Largest gap in scaffolds 0
Smallest gap in scaffolds 0
Base composition (A:C:G:T) 627,800:397,884:399,253:627,504
GC content % 38.84
# soft-masked bases 0
# segments 84
Total segment length 2,052,441
Average segment length 24,433.82
# gaps 0
# paths 84
# edges 8
Average degree 0.10
# connected components 2
Largest connected component length 96,664
# dead ends 162
# disconnected components 78
Total length disconnected components 1,895,760
# separated components 80
# bubbles 0
# circular segments 0
# circular paths 0
Scaffold N10 93,875
Scaffold N20 38,474
Scaffold N30 26,760
Scaffold N40 24,256
Scaffold N50 22,011
Scaffold N60 20,526
Scaffold N70 19,727
Scaffold N80 19,045
Scaffold N90 17,730
Scaffold N100 15,406
Scaffold L10 2
Scaffold L20 7
Scaffold L30 14
Scaffold L40 22
Scaffold L50 31
Scaffold L60 40
Scaffold L70 51
Scaffold L80 61
Scaffold L90 72
Scaffold L100 84
Scaffold NG10 46,449
Scaffold NG20 31,085
Scaffold NG30 25,225
Scaffold NG40 23,513
Scaffold NG50 20,895
Scaffold NG60 19,871
Scaffold NG70 19,102
Scaffold NG80 17,885
Scaffold NG90 0
Scaffold NG100 0
Scaffold LG10 3
Scaffold LG20 8
Scaffold LG30 16
Scaffold LG40 26
Scaffold LG50 36
Scaffold LG60 47
Scaffold LG70 59
Scaffold LG80 71
Scaffold LG90 0
Scaffold LG100 0
Contig N10 93,875
Contig N20 38,474
Contig N30 26,760
Contig N40 24,256
Contig N50 22,011
Contig N60 20,526
Contig N70 19,727
Contig N80 19,045
Contig N90 17,730
Contig N100 15,406
Contig L10 2
Contig L20 7
Contig L30 14
Contig L40 22
Contig L50 31
Contig L60 40
Contig L70 51
Contig L80 61
Contig L90 72
Contig L100 84
Contig NG10 46,449
Contig NG20 31,085
Contig NG30 25,225
Contig NG40 23,513
Contig NG50 20,895
Contig NG60 19,871
Contig NG70 19,102
Contig NG80 17,885
Contig NG90 0
Contig NG100 0
Contig LG10 3
Contig LG20 8
Contig LG30 16
Contig LG40 26
Contig LG50 36
Contig LG60 47
Contig LG70 59
Contig LG80 71
Contig LG90 0
Contig LG100 0
Gap N10 0
Gap N20 0
Gap N30 0
Gap N40 0
Gap N50 0
Gap N60 0
Gap N70 0
Gap N80 0
Gap N90 0
Gap N100 0
Gap L10 0
Gap L20 0
Gap L30 0
Gap L40 0
Gap L50 0
Gap L60 0
Gap L70 0
Gap L80 0
Gap L90 0
Gap L100 0
')
2024-12-16 05:13:36 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:
2024-12-16 04:55:33 INFO: ***** Start a BUSCO v5.8.0 analysis, current time: 12/16/2024 04:55:33 *****2024-12-16 04:55:33 INFO: Configuring BUSCO with local environment2024-12-16 04:55:33 INFO: Running genome mode2024-12-16 04:55:39 INFO: Input file is /tmp/tmpb1mrmk_7/files/3/c/5/dataset_3c5f52df-9e1b-4009-ba59-9112e1b6d028.dat2024-12-16 04:55:39 WARNING: Option evalue was provided but is not used in the selected run mode, euk_genome_met2024-12-16 04:55:39 WARNING: Option limit was provided but is not used in the selected run mode, euk_genome_met2024-12-16 04:55:40 INFO: Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)2024-12-16 04:55:40 INFO: Running 1 job(s) on bbtools, starting at 12/16/2024 04:55:402024-12-16 04:55:41 INFO: [bbtools] 1 of 1 task(s) completed2024-12-16 04:55:41 INFO: Running 1 job(s) on metaeuk, starting at 12/16/2024 04:55:412024-12-16 05:00:51 INFO: [metaeuk] 1 of 1 task(s) completed2024-12-16 05:00:51 INFO: ***** Run HMMER on gene sequences *****2024-12-16 05:00:51 INFO: Running 3354 job(s) on hmmsearch, starting at 12/16/2024 05:00:512024-12-16 05:01:03 INFO: [hmmsearch] 336 of 3354 task(s) completed2024-12-16 05:01:14 INFO: [hmmsearch] 671 of 3354 task(s) completed2024-12-16 05:01:26 INFO: [hmmsearch] 1007 of 3354 task(s) completed2024-12-16 05:01:37 INFO: [hmmsearch] 1342 of 3354 task(s) completed2024-12-16 05:01:46 INFO: [hmmsearch] 1677 of 3354 task(s) completed2024-12-16 05:01:56 INFO: [hmmsearch] 2013 of 3354 task(s) completed2024-12-16 05:02:07 INFO: [hmmsearch] 2348 of 3354 task(s) completed2024-12-16 05:02:16 INFO: [hmmsearch] 2684 of 3354 task(s) completed2024-12-16 05:02:38 INFO: [hmmsearch] 3019 of 3354 task(s) completed2024-12-16 05:03:09 INFO: [hmmsearch] 3354 of 3354 task(s) completed2024-12-16 05:03:09 INFO: 59 exons in total2024-12-16 05:03:10 INFO: Extracting missing and fragmented buscos from the file refseq_db.faa...2024-12-16 05:04:58 INFO: Running 1 job(s) on metaeuk, starting at 12/16/2024 05:04:582024-12-16 05:12:57 INFO: [metaeuk] 1 of 1 task(s) completed2024-12-16 05:12:57 INFO: ***** Run HMMER on gene sequences *****2024-12-16 05:12:57 INFO: Running 3314 job(s) on hmmsearch, starting at 12/16/2024 05:12:572024-12-16 05:13:01 INFO: [hmmsearch] 332 of 3314 task(s) completed2024-12-16 05:13:05 INFO: [hmmsearch] 663 of 3314 task(s) completed2024-12-16 05:13:08 INFO: [hmmsearch] 995 of 3314 task(s) completed2024-12-16 05:13:11 INFO: [hmmsearch] 1326 of 3314 task(s) completed2024-12-16 05:13:15 INFO: [hmmsearch] 1657 of 3314 task(s) completed2024-12-16 05:13:19 INFO: [hmmsearch] 1989 of 3314 task(s) completed2024-12-16 05:13:22 INFO: [hmmsearch] 2320 of 3314 task(s) completed2024-12-16 05:13:26 INFO: [hmmsearch] 2652 of 3314 task(s) completed2024-12-16 05:13:29 INFO: [hmmsearch] 2983 of 3314 task(s) completed2024-12-16 05:13:33 INFO: [hmmsearch] 3314 of 3314 task(s) completed2024-12-16 05:13:33 INFO: 4 candidate overlapping regions found2024-12-16 05:13:33 INFO: 65 exons in total2024-12-16 05:13:33 INFO: Results: C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354 2024-12-16 05:13:34 INFO: --------------------------------------------------- |Results from dataset vertebrata_odb10 | --------------------------------------------------- |C:1.2%[S:1.2%,D:0.0%],F:0.4%,M:98.4%,n:3354 | |40 Complete BUSCOs (C) | |39 Complete and single-copy BUSCOs (S) | |1 Complete and duplicated BUSCOs (D) | |15 Fragmented BUSCOs (F) | |3299 Missing BUSCOs (M) | |3354 Total BUSCO groups searched | ---------------------------------------------------2024-12-16 05:13:34 INFO: BUSCO analysis done with WARNING(s). Total running time: 1074 seconds***** Summary of warnings: *****2024-12-16 04:55:39 WARNING:busco.BuscoConfig Option evalue was provided but is not used in the selected run mode, euk_genome_met2024-12-16 04:55:39 WARNING:busco.BuscoConfig Option limit was provided but is not used in the selected run mode, euk_genome_met2024-12-16 05:13:34 INFO: Results written in /tmp/tmpb1mrmk_7/job_working_directory/000/27/working/busco_galaxy2024-12-16 05:13:34 INFO: For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html2024-12-16 05:13:34 INFO: Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCOtotal 140drwxr-xr-x 5 1001 118 4096 Dec 16 04:55 busco_sequences-rw-r--r-- 1 1001 118 76855 Dec 16 05:13 full_table.tsvdrwxr-xr-x 4 1001 118 4096 Dec 16 05:03 hmmer_outputdrwxr-xr-x 4 1001 118 4096 Dec 16 05:13 metaeuk_output-rw-r--r-- 1 1001 118 42328 Dec 16 05:13 missing_busco_list.tsv-rw-r--r-- 1 1001 118 2953 Dec 16 05:13 short_summary.json-rw-r--r-- 1 1001 118 969 Dec 16 05:13 short_summary.txt2024-12-16 05:13:34 INFO: ****************** Start plot generation at 12/16/2024 05:13:34 ******************2024-12-16 05:13:34 INFO: Load data ...2024-12-16 05:13:34 INFO: Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully2024-12-16 05:13:34 INFO: Generate the R code ...2024-12-16 05:13:34 INFO: Run the R code ...2024-12-16 05:13:36 INFO: [1] "Plotting the figure ..."[1] "Done"2024-12-16 05:13:36 INFO: Plot generation done. Total running time: 1.9713163375854492 seconds2024-12-16 05:13:36 INFO: Results written in BUSCO_summaries/
c3/2052441c2/1000000c3/1000000Computing 3 new columns with instructions ['c3/2052441;;', 'c2/1000000;;', 'c3/1000000;;']Computed new column values for 100.00% of 84 lines written.
c3/34014c2/1000000c3/1000000Computing 3 new columns with instructions ['c3/34014;;', 'c2/1000000;;', 'c3/1000000;;']Computed new column values for 100.00% of 3 lines written.
Warning message:In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honoredWarning message:package ‘ggplot2’ was built under R version 4.1.3 Warning message:Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.ℹ Please use `linewidth` instead.
Warning message:In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : OS reports request to set locale to "en_US.UTF-8" cannot be honoredWarning message:package ‘ggplot2’ was built under R version 4.1.3 Warning message:Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.ℹ Please use `linewidth` instead.
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Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3. 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/bgruening/hifiasm/hifiasm/0.19.9+galaxy0
should be updated totoolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.20.0+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0
should be updated totoolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0
should be updated totoolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0
The workflow release number has been updated from 0.2.2 to 0.2.3.
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.