Add workflow: genome annotation with Maker #631

rlibouba · 2024-12-11T09:33:21Z

Hello,
I would like to propose this workflow for annotating a genome from the GTN "Genome annotation with Maker (short)".

Thank you! Have a nice day!

wm75 · 2024-12-12T10:19:06Z

This looks really cool already, thanks!

When I'm importing the WF on Galaxy Europe, it complains about

So I guess that needs to be fixed.

In the README I would not discuss inputs/outputs per tool but at the WF level to avoid redundancy.
You can just list the inputs, their expected format and what the WF will use them for.
Likewise, you can have one list of all outputs, what they are for and (if that's relevant/helpful) which tool produced them.

Without knowing too much about the details of the WF, would a MultiQC combined report of some of the results make sense?

wm75 · 2024-12-12T10:21:53Z

workflows/genome_annotation/annotation_maker/Genome_annotation_with_maker_short_tests.yml

+      filetype: snaphmm
+
+
+  outputs:


Most of these outputs should be exactly reproducible text files. It's better to check them for actual content than just for approx. size.
You can test the presence of specific lines of text, for example.

github-actions · 2024-12-17T17:43:00Z

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_maker_short.ga_0

github-actions · 2024-12-18T10:13:48Z

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_maker_short.ga_0

github-actions · 2024-12-18T11:01:53Z

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_maker_short.ga_0

github-actions · 2024-12-18T14:46:54Z

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_maker_short.ga_0

Problems:

Output with path /tmp/tmptsq1_ptk/Busco on data 15 GFF__7e7e240c-881c-416b-a5ba-93611220de80 different than expected
Expected text 'snap-NC_003421.2-processed-gene-12.94-mRNA-1' in output ('##gff-version 3
snap-NC_003421.2-processed-gene-12.33-mRNA-1	MetaEuk	gene	6745	8037	61	+	.	Target_ID=118701at4751_402676_1:00055d;TCS_ID=118701at4751_402676_1:00055d|snap-NC_003421.2-processed-gene-12.33-mRNA-1|+|6744
snap-NC_003421.2-processed-gene-12.33-mRNA-1	MetaEuk	gene	6745	8037	61	+	.	Target_ID=118701at4751_402676_1:00055d;TCS_ID=118701at4751_402676_1:00055d|snap-NC_003421.2-processed-gene-12.33-mRNA-1|+|6744
snap-NC_003421.2-processed-gene-4.105-mRNA-1	MetaEuk	gene	2380	2757	123	+	.	Target_ID=119833at4751_61395_1:00030d;TCS_ID=119833at4751_61395_1:00030d|snap-NC_003421.2-processed-gene-4.105-mRNA-1|+|2379
snap-NC_003421.2-processed-gene-4.105-mRNA-1	MetaEuk	gene	2380	2757	123	+	.	Target_ID=119833at4751_61395_1:00030d;TCS_ID=119833at4751_61395_1:00030d|snap-NC_003421.2-processed-gene-4.105-mRNA-1|+|2379
maker-NC_003421.2-augustus-gene-18.1-mRNA-1	MetaEuk	gene	95	802	349	+	.	Target_ID=189573at4751_483514_1:00063e;TCS_ID=189573at4751_483514_1:00063e|maker-NC_003421.2-augustus-gene-18.1-mRNA-1|+|94
maker-NC_003421.2-augustus-gene-18.1-mRNA-1	MetaEuk	gene	95	802	349	+	.	Target_ID=189573at4751_483514_1:00063e;TCS_ID=189573at4751_483514_1:00063e|maker-NC_003421.2-augustus-gene-18.1-mRNA-1|+|94
snap-NC_003421.2-processed-gene-1.33-mRNA-1	MetaEuk	gene	55	969	203	+	.	Target_ID=198196at4751_13706_1:00058d;TCS_ID=198196at4751_13706_1:00058d|snap-NC_003421.2-processed-gene-1.33-mRNA-1|+|54
snap-NC_003421.2-processed-gene-1.33-mRNA-1	MetaEuk	gene	55	969	203	+	.	Target_ID=198196at4751_13706_1:00058d;TCS_ID=198196at4751_13706_1:00058d|snap-NC_003421.2-processed-gene-1.33-mRNA-1|+|54
snap-NC_003421.2-processed-gene-13.65-mRNA-1	MetaEuk	gene	292	1110	76	+	.	Target_ID=320638at4751_684364_1:000687;TCS_ID=320638at4751_684364_1:000687|snap-NC_003421.2-processed-gene-13.65-mRNA-1|+|291
maker-NC_003421.2-augustus-gene-23.147-mRNA-1	MetaEuk	gene	151	564	53	+	.	Target_ID=396842at4751_881290_1:0007d0;TCS_ID=396842at4751_881290_1:0007d0|maker-NC_003421.2-augustus-gene-23.147-mRNA-1|+|150
snap-NC_003421.2-processed-gene-16.18-mRNA-1	MetaEuk	gene	490	1224	88	+	.	Target_ID=4466at4751_200324_1:000152;TCS_ID=4466at4751_200324_1:000152|snap-NC_003421.2-processed-gene-16.18-mRNA-1|+|489
maker-NC_003421.2-augustus-gene-5.100-mRNA-1	MetaEuk	gene	210	3200	224	+	.	Target_ID=56432at4751_1408658_1:000b00;TCS_ID=56432at4751_1408658_1:000b00|maker-NC_003421.2-augustus-gene-5.100-mRNA-1|+|209
maker-NC_003421.2-augustus-gene-5.100-mRNA-1	MetaEuk	gene	210	3200	224	+	.	Target_ID=56432at4751_1408658_1:000b00;TCS_ID=56432at4751_1408658_1:000b00|maker-NC_003421.2-augustus-gene-5.100-mRNA-1|+|209
augustus-NC_003421.2-processed-gene-15.71-mRNA-1	MetaEuk	gene	79	2817	143	+	.	Target_ID=6377at4751_1128425_1:0022e4;TCS_ID=6377at4751_1128425_1:0022e4|augustus-NC_003421.2-processed-gene-15.71-mRNA-1|+|78
augustus-NC_003421.2-processed-gene-15.71-mRNA-1	MetaEuk	gene	79	2817	143	+	.	Target_ID=6377at4751_1128425_1:0022e4;TCS_ID=6377at4751_1128425_1:0022e4|augustus-NC_003421.2-processed-gene-15.71-mRNA-1|+|78
maker-NC_003421.2-snap-gene-14.45-mRNA-1	MetaEuk	gene	56	2500	709	+	.	Target_ID=76975at4751_483514_1:00079d;TCS_ID=76975at4751_483514_1:00079d|maker-NC_003421.2-snap-gene-14.45-mRNA-1|+|55
maker-NC_003421.2-snap-gene-14.45-mRNA-1	MetaEuk	gene	56	2500	709	+	.	Target_ID=76975at4751_483514_1:00079d;TCS_ID=76975at4751_483514_1:00079d|maker-NC_003421.2-snap-gene-14.45-mRNA-1|+|55
maker-NC_003421.2-augustus-gene-12.92-mRNA-1	MetaEuk	gene	1	2754	442	+	.	Target_ID=85793at4751_653667_1:000c86;TCS_ID=85793at4751_653667_1:000c86|maker-NC_003421.2-augustus-gene-12.92-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-12.92-mRNA-1	MetaEuk	gene	1	2754	442	+	.	Target_ID=85793at4751_653667_1:000c86;TCS_ID=85793at4751_653667_1:000c86|maker-NC_003421.2-augustus-gene-12.92-mRNA-1|+|0
maker-NC_003421.2-snap-gene-15.45-mRNA-1	MetaEuk	gene	1134	1880	337	-	.	Target_ID=298379at4751_653667_1:000bde;TCS_ID=298379at4751_653667_1:000bde|maker-NC_003421.2-snap-gene-15.45-mRNA-1|-|1133
snap-NC_003421.2-processed-gene-15.30-mRNA-1	MetaEuk	gene	58	804	337	+	.	Target_ID=298379at4751_653667_1:000bde;TCS_ID=298379at4751_653667_1:000bde|snap-NC_003421.2-processed-gene-15.30-mRNA-1|+|57
snap-NC_003421.2-processed-gene-13.73-mRNA-1	MetaEuk	gene	1	1653	933	+	.	Target_ID=101133at4751_483514_1:001111;TCS_ID=101133at4751_483514_1:001111|snap-NC_003421.2-processed-gene-13.73-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-5.79-mRNA-1	MetaEuk	gene	395	3025	1345	+	.	Target_ID=103183at4751_653667_1:00105f;TCS_ID=103183at4751_653667_1:00105f|augustus-NC_003421.2-processed-gene-5.79-mRNA-1|+|394
snap-NC_003421.2-processed-gene-5.5-mRNA-1	MetaEuk	gene	1	3042	1347	+	.	Target_ID=103461at4751_483514_1:00091c;TCS_ID=103461at4751_483514_1:00091c|snap-NC_003421.2-processed-gene-5.5-mRNA-1|+|0
snap-NC_003421.2-processed-gene-22.10-mRNA-1	MetaEuk	gene	1	4125	1542	+	.	Target_ID=11636at4751_653667_1:000a79;TCS_ID=11636at4751_653667_1:000a79|snap-NC_003421.2-processed-gene-22.10-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-10.35-mRNA-1	MetaEuk	gene	22	2298	1103	+	.	Target_ID=122507at4751_483514_1:000f4c;TCS_ID=122507at4751_483514_1:000f4c|augustus-NC_003421.2-processed-gene-10.35-mRNA-1|+|21
snap-NC_003421.2-processed-gene-1.41-mRNA-1	MetaEuk	gene	1	3282	1315	+	.	Target_ID=126037at4751_653667_1:001091;TCS_ID=126037at4751_653667_1:001091|snap-NC_003421.2-processed-gene-1.41-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-19.53-mRNA-1	MetaEuk	gene	146	1849	978	+	.	Target_ID=126256at4751_653667_1:000aef;TCS_ID=126256at4751_653667_1:000aef|maker-NC_003421.2-augustus-gene-19.53-mRNA-1|+|145
snap-NC_003421.2-processed-gene-20.57-mRNA-1	MetaEuk	gene	1	4896	2105	+	.	Target_ID=130930at4751_653667_1:000b5f;TCS_ID=130930at4751_653667_1:000b5f|snap-NC_003421.2-processed-gene-20.57-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-3.0-mRNA-1	MetaEuk	gene	405	2126	777	+	.	Target_ID=130976at4751_483514_1:0007e4;TCS_ID=130976at4751_483514_1:0007e4|maker-NC_003421.2-augustus-gene-3.0-mRNA-1|+|404
maker-NC_003421.2-augustus-gene-3.11-mRNA-1	MetaEuk	gene	305	1552	745	+	.	Target_ID=165243at4751_653667_1:00104c;TCS_ID=165243at4751_653667_1:00104c|maker-NC_003421.2-augustus-gene-3.11-mRNA-1|+|304
maker-NC_003421.2-snap-gene-14.51-mRNA-1	MetaEuk	gene	124	1689	921	+	.	Target_ID=167498at4751_653667_1:000a63;TCS_ID=167498at4751_653667_1:000a63|maker-NC_003421.2-snap-gene-14.51-mRNA-1|+|123
snap-NC_003421.2-processed-gene-23.35-mRNA-1	MetaEuk	gene	46	1779	844	+	.	Target_ID=168092at4751_653667_1:001122;TCS_ID=168092at4751_653667_1:001122|snap-NC_003421.2-processed-gene-23.35-mRNA-1|+|45
snap-NC_003421.2-processed-gene-21.19-mRNA-1	MetaEuk	gene	1	1299	747	+	.	Target_ID=171238at4751_653667_1:000c64;TCS_ID=171238at4751_653667_1:000c64|snap-NC_003421.2-processed-gene-21.19-mRNA-1|+|0
snap-NC_003421.2-processed-gene-9.98-mRNA-1	MetaEuk	gene	85	3054	1363	+	.	Target_ID=17174at4751_483514_1:000959;TCS_ID=17174at4751_483514_1:000959|snap-NC_003421.2-processed-gene-9.98-mRNA-1|+|84
snap-NC_003421.2-processed-gene-3.83-mRNA-1	MetaEuk	gene	13	1818	724	+	.	Target_ID=173428at4751_483514_1:000b3b;TCS_ID=173428at4751_483514_1:000b3b|snap-NC_003421.2-processed-gene-3.83-mRNA-1|+|12
snap-NC_003421.2-processed-gene-4.115-mRNA-1	MetaEuk	gene	16	1542	629	+	.	Target_ID=176648at4751_483514_1:000b29;TCS_ID=176648at4751_483514_1:000b29|snap-NC_003421.2-processed-gene-4.115-mRNA-1|+|15
maker-NC_003421.2-snap-gene-17.42-mRNA-1	MetaEuk	gene	176	1633	846	+	.	Target_ID=179437at4751_653667_1:0009e6;TCS_ID=179437at4751_653667_1:0009e6|maker-NC_003421.2-snap-gene-17.42-mRNA-1|+|175
maker-NC_003421.2-augustus-gene-20.44-mRNA-1	MetaEuk	gene	258	1160	505	+	.	Target_ID=183801at4751_653667_1:000bc2;TCS_ID=183801at4751_653667_1:000bc2|maker-NC_003421.2-augustus-gene-20.44-mRNA-1|+|257
maker-NC_003421.2-augustus-gene-6.35-mRNA-1	MetaEuk	gene	78	2381	1122	+	.	Target_ID=185196at4751_653667_1:00101f;TCS_ID=185196at4751_653667_1:00101f|maker-NC_003421.2-augustus-gene-6.35-mRNA-1|+|77
augustus-NC_003421.2-processed-gene-13.36-mRNA-1	MetaEuk	gene	1	3126	879	+	.	Target_ID=186701at4751_653667_1:000c7d;TCS_ID=186701at4751_653667_1:000c7d|augustus-NC_003421.2-processed-gene-13.36-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.63-mRNA-1	MetaEuk	gene	37	1200	739	+	.	Target_ID=188070at4751_653667_1:0010e8;TCS_ID=188070at4751_653667_1:0010e8|maker-NC_003421.2-augustus-gene-4.63-mRNA-1|+|36
maker-NC_003421.2-augustus-gene-21.55-mRNA-1	MetaEuk	gene	219	2036	880	+	.	Target_ID=189234at4751_653667_1:000c0f;TCS_ID=189234at4751_653667_1:000c0f|maker-NC_003421.2-augustus-gene-21.55-mRNA-1|+|218
maker-NC_003421.2-augustus-gene-23.143-mRNA-1	MetaEuk	gene	141	1439	712	+	.	Target_ID=190183at4751_653667_1:0010d8;TCS_ID=190183at4751_653667_1:0010d8|maker-NC_003421.2-augustus-gene-23.143-mRNA-1|+|140
snap-NC_003421.2-processed-gene-23.46-mRNA-1	MetaEuk	gene	1	1956	936	+	.	Target_ID=190475at4751_653667_1:00113c;TCS_ID=190475at4751_653667_1:00113c|snap-NC_003421.2-processed-gene-23.46-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-8.68-mRNA-1	MetaEuk	gene	1	969	381	+	.	Target_ID=200331at4751_653667_1:0010d1;TCS_ID=200331at4751_653667_1:0010d1|augustus-NC_003421.2-processed-gene-8.68-mRNA-1|+|0
maker-NC_003421.2-snap-gene-7.36-mRNA-1	MetaEuk	gene	63	1217	657	+	.	Target_ID=203109at4751_483514_1:0008b9;TCS_ID=203109at4751_483514_1:0008b9|maker-NC_003421.2-snap-gene-7.36-mRNA-1|+|62
snap-NC_003421.2-processed-gene-18.93-mRNA-1	MetaEuk	gene	1	1182	707	+	.	Target_ID=204087at4751_483514_1:0009f3;TCS_ID=204087at4751_483514_1:0009f3|snap-NC_003421.2-processed-gene-18.93-mRNA-1|+|0
snap-NC_003421.2-processed-gene-4.104-mRNA-1	MetaEuk	gene	1	2226	874	+	.	Target_ID=204341at4751_483514_1:0008f8;TCS_ID=204341at4751_483514_1:0008f8|snap-NC_003421.2-processed-gene-4.104-mRNA-1|+|0
snap-NC_003421.2-processed-gene-10.5-mRNA-1	MetaEuk	gene	4	1209	555	+	.	Target_ID=209619at4751_653667_1:00112e;TCS_ID=209619at4751_653667_1:00112e|snap-NC_003421.2-processed-gene-10.5-mRNA-1|+|3
snap-NC_003421.2-processed-gene-17.97-mRNA-1	MetaEuk	gene	7	1686	771	+	.	Target_ID=211442at4751_483514_1:001292;TCS_ID=211442at4751_483514_1:001292|snap-NC_003421.2-processed-gene-17.97-mRNA-1|+|6
snap-NC_003421.2-processed-gene-3.97-mRNA-1	MetaEuk	gene	79	1287	574	+	.	Target_ID=216683at4751_483514_1:000954;TCS_ID=216683at4751_483514_1:000954|snap-NC_003421.2-processed-gene-3.97-mRNA-1|+|78
maker-NC_003421.2-augustus-gene-7.63-mRNA-1	MetaEuk	gene	133	1488	791	+	.	Target_ID=216747at4751_653667_1:0010ff;TCS_ID=216747at4751_653667_1:0010ff|maker-NC_003421.2-augustus-gene-7.63-mRNA-1|+|132
augustus-NC_003421.2-processed-gene-5.71-mRNA-1	MetaEuk	gene	95	2800	1405	+	.	Target_ID=21689at4751_653667_1:0010d2;TCS_ID=21689at4751_653667_1:0010d2|augustus-NC_003421.2-processed-gene-5.71-mRNA-1|+|94
snap-NC_003421.2-processed-gene-9.105-mRNA-1	MetaEuk	gene	1	1308	638	+	.	Target_ID=225535at4751_483514_1:0008ee;TCS_ID=225535at4751_483514_1:0008ee|snap-NC_003421.2-processed-gene-9.105-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-7.56-mRNA-1	MetaEuk	gene	53	4708	1367	+	.	Target_ID=234548at4751_483514_1:000c48;TCS_ID=234548at4751_483514_1:000c48|maker-NC_003421.2-augustus-gene-7.56-mRNA-1|+|52
maker-NC_003421.2-snap-gene-2.18-mRNA-1	MetaEuk	gene	492	1916	400	+	.	Target_ID=237276at4751_402676_1:0003b9;TCS_ID=237276at4751_402676_1:0003b9|maker-NC_003421.2-snap-gene-2.18-mRNA-1|+|491
snap-NC_003421.2-processed-gene-9.106-mRNA-1	MetaEuk	gene	1	1065	594	+	.	Target_ID=237533at4751_653667_1:0010be;TCS_ID=237533at4751_653667_1:0010be|snap-NC_003421.2-processed-gene-9.106-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.76-mRNA-1	MetaEuk	gene	673	2325	767	+	.	Target_ID=241079at4751_483514_1:000ccb;TCS_ID=241079at4751_483514_1:000ccb|maker-NC_003421.2-augustus-gene-4.76-mRNA-1|+|672
maker-NC_003421.2-augustus-gene-16.113-mRNA-1	MetaEuk	gene	16	1869	711	+	.	Target_ID=247129at4751_483514_1:000ff4;TCS_ID=247129at4751_483514_1:000ff4|maker-NC_003421.2-augustus-gene-16.113-mRNA-1|+|15
snap-NC_003421.2-processed-gene-14.99-mRNA-1	MetaEuk	gene	1	1083	551	+	.	Target_ID=247383at4751_483514_1:000531;TCS_ID=247383at4751_483514_1:000531|snap-NC_003421.2-processed-gene-14.99-mRNA-1|+|0
maker-NC_003421.2-snap-gene-6.71-mRNA-1	MetaEuk	gene	97	972	200	+	.	Target_ID=252314at4751_1507870_1:001c80;TCS_ID=252314at4751_1507870_1:001c80|maker-NC_003421.2-snap-gene-6.71-mRNA-1|+|96
snap-NC_003421.2-processed-gene-23.17-mRNA-1	MetaEuk	gene	1	1794	674	+	.	Target_ID=264164at4751_653667_1:001020;TCS_ID=264164at4751_653667_1:001020|snap-NC_003421.2-processed-gene-23.17-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-1.46-mRNA-1	MetaEuk	gene	1	1278	563	+	.	Target_ID=265325at4751_653667_1:000877;TCS_ID=265325at4751_653667_1:000877|augustus-NC_003421.2-processed-gene-1.46-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-21.46-mRNA-1	MetaEuk	gene	46	1647	802	+	.	Target_ID=281920at4751_483514_1:000457;TCS_ID=281920at4751_483514_1:000457|maker-NC_003421.2-augustus-gene-21.46-mRNA-1|+|45
maker-NC_003421.2-augustus-gene-8.50-mRNA-1	MetaEuk	gene	64	2553	1089	+	.	Target_ID=284377at4751_653667_1:001120;TCS_ID=284377at4751_653667_1:001120|maker-NC_003421.2-augustus-gene-8.50-mRNA-1|+|63
snap-NC_003421.2-processed-gene-21.9-mRNA-1	MetaEuk	gene	1545	2417	484	+	.	Target_ID=289666at4751_653667_1:000b78;TCS_ID=289666at4751_653667_1:000b78|snap-NC_003421.2-processed-gene-21.9-mRNA-1|+|1544
augustus-NC_003421.2-processed-gene-5.90-mRNA-1	MetaEuk	gene	1	852	474	+	.	Target_ID=295692at4751_653667_1:0010dd;TCS_ID=295692at4751_653667_1:0010dd|augustus-NC_003421.2-processed-gene-5.90-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-21.52-mRNA-1	MetaEuk	gene	127	1455	514	+	.	Target_ID=297671at4751_483514_1:0000ad;TCS_ID=297671at4751_483514_1:0000ad|maker-NC_003421.2-augustus-gene-21.52-mRNA-1|+|126
maker-NC_003421.2-snap-gene-0.26-mRNA-1	MetaEuk	gene	260	1132	460	+	.	Target_ID=299330at4751_483514_1:000f99;TCS_ID=299330at4751_483514_1:000f99|maker-NC_003421.2-snap-gene-0.26-mRNA-1|+|259
maker-NC_003421.2-snap-gene-11.39-mRNA-1	MetaEuk	gene	73	1146	654	+	.	Target_ID=299509at4751_653667_1:000d1c;TCS_ID=299509at4751_653667_1:000d1c|maker-NC_003421.2-snap-gene-11.39-mRNA-1|+|72
maker-NC_003421.2-augustus-gene-16.99-mRNA-1	MetaEuk	gene	1	918	555	+	.	Target_ID=299583at4751_483514_1:00051f;TCS_ID=299583at4751_483514_1:00051f|maker-NC_003421.2-augustus-gene-16.99-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.66-mRNA-1	MetaEuk	gene	2915	3778	461	+	.	Target_ID=304341at4751_653667_1:00104e;TCS_ID=304341at4751_653667_1:00104e|maker-NC_003421.2-augustus-gene-4.66-mRNA-1|+|2914
maker-NC_003421.2-augustus-gene-19.45-mRNA-1	MetaEuk	gene	47	2662	1201	+	.	Target_ID=305061at4751_653667_1:000ab2;TCS_ID=305061at4751_653667_1:000ab2|maker-NC_003421.2-augustus-gene-19.45-mRNA-1|+|46
maker-NC_003421.2-augustus-gene-13.61-mRNA-1	MetaEuk	gene	57	1367	632	+	.	Target_ID=306594at4751_653667_1:000986;TCS_ID=306594at4751_653667_1:000986|maker-NC_003421.2-augustus-gene-13.61-mRNA-1|+|56
maker-NC_003421.2-snap-gene-2.14-mRNA-1	MetaEuk	gene	7	2199	1034	+	.	Target_ID=310718at4751_653667_1:000ffc;TCS_ID=310718at4751_653667_1:000ffc|maker-NC_003421.2-snap-gene-2.14-mRNA-1|+|6
maker-NC_003421.2-augustus-gene-1.104-mRNA-1	MetaEuk	gene	336	1130	400	+	.	Target_ID=312209at4751_653667_1:00105d;TCS_ID=312209at4751_653667_1:00105d|maker-NC_003421.2-augustus-gene-1.104-mRNA-1|+|335
snap-NC_003421.2-processed-gene-14.91-mRNA-1	MetaEuk	gene	1	3294	1030	+	.	Target_ID=31256at4751_653667_1:000a33;TCS_ID=31256at4751_653667_1:000a33|snap-NC_003421.2-processed-gene-14.91-mRNA-1|+|0
snap-NC_003421.2-processed-gene-14.97-mRNA-1	MetaEuk	gene	55	957	529	+	.	Target_ID=321728at4751_653667_1:000c26;TCS_ID=321728at4751_653667_1:000c26|snap-NC_003421.2-processed-gene-14.97-mRNA-1|+|54
maker-NC_003421.2-augustus-gene-14.61-mRNA-1	MetaEuk	gene	118	1137	631	+	.	Target_ID=323327at4751_653667_1:000c51;TCS_ID=323327at4751_653667_1:000c51|maker-NC_003421.2-augustus-gene-14.61-mRNA-1|+|117
maker-NC_003421.2-augustus-gene-1.93-mRNA-1	MetaEuk	gene	1539	2384	450	+	.	Target_ID=325992at4751_653667_1:00083f;TCS_ID=325992at4751_653667_1:00083f|maker-NC_003421.2-augustus-gene-1.93-mRNA-1|+|1538
maker-NC_003421.2-augustus-gene-19.56-mRNA-1	MetaEuk	gene	1	936	492	+	.	Target_ID=327884at4751_483514_1:00063c;TCS_ID=327884at4751_483514_1:00063c|maker-NC_003421.2-augustus-gene-19.56-mRNA-1|+|0
snap-NC_003421.2-processed-gene-21.6-mRNA-1	MetaEuk	gene	1	759	487	+	.	Target_ID=331763at4751_483514_1:000028;TCS_ID=331763at4751_483514_1:000028|snap-NC_003421.2-processed-gene-21.6-mRNA-1|+|0
snap-NC_003421.2-processed-gene-1.10-mRNA-1	MetaEuk	gene	1	1902	1054	+	.	Target_ID=332876at4751_653667_1:0010fc;TCS_ID=332876at4751_653667_1:0010fc|snap-NC_003421.2-processed-gene-1.10-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-4.70-mRNA-1	MetaEuk	gene	117	1016	547	+	.	Target_ID=335719at4751_653667_1:0010bc;TCS_ID=335719at4751_653667_1:0010bc|maker-NC_003421.2-augustus-gene-4.70-mRNA-1|+|116
snap-NC_003421.2-processed-gene-13.94-mRNA-1	MetaEuk	gene	1	1020	594	+	.	Target_ID=336181at4751_653667_1:0008f0;TCS_ID=336181at4751_653667_1:0008f0|snap-NC_003421.2-processed-gene-13.94-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-8.49-mRNA-1	MetaEuk	gene	245	880	274	+	.	Target_ID=336187at4751_653667_1:001126;TCS_ID=336187at4751_653667_1:001126|maker-NC_003421.2-augustus-gene-8.49-mRNA-1|+|244
snap-NC_003421.2-processed-gene-5.33-mRNA-1	MetaEuk	gene	7	2760	1653	+	.	Target_ID=33984at4751_653667_1:001087;TCS_ID=33984at4751_653667_1:001087|snap-NC_003421.2-processed-gene-5.33-mRNA-1|+|6
augustus-NC_003421.2-processed-gene-7.2-mRNA-1	MetaEuk	gene	1	1086	551	+	.	Target_ID=348111at4751_653667_1:001029;TCS_ID=348111at4751_653667_1:001029|augustus-NC_003421.2-processed-gene-7.2-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-13.54-mRNA-1	MetaEuk	gene	38	895	541	+	.	Target_ID=351482at4751_653667_1:000cd2;TCS_ID=351482at4751_653667_1:000cd2|maker-NC_003421.2-augustus-gene-13.54-mRNA-1|+|37
maker-NC_003421.2-snap-gene-22.56-mRNA-1	MetaEuk	gene	10	738	343	+	.	Target_ID=351646at4751_653667_1:000ab5;TCS_ID=351646at4751_653667_1:000ab5|maker-NC_003421.2-snap-gene-22.56-mRNA-1|+|9
maker-NC_003421.2-augustus-gene-22.98-mRNA-1	MetaEuk	gene	28	759	477	+	.	Target_ID=351858at4751_483514_1:0005da;TCS_ID=351858at4751_483514_1:0005da|maker-NC_003421.2-augustus-gene-22.98-mRNA-1|+|27
maker-NC_003421.2-augustus-gene-17.61-mRNA-1	MetaEuk	gene	42	1655	739	+	.	Target_ID=355454at4751_653667_1:000a48;TCS_ID=355454at4751_653667_1:000a48|maker-NC_003421.2-augustus-gene-17.61-mRNA-1|+|41
maker-NC_003421.2-augustus-gene-21.48-mRNA-1	MetaEuk	gene	177	1010	430	+	.	Target_ID=355781at4751_483514_1:00043e;TCS_ID=355781at4751_483514_1:00043e|maker-NC_003421.2-augustus-gene-21.48-mRNA-1|+|176
snap-NC_003421.2-processed-gene-6.22-mRNA-1	MetaEuk	gene	1	648	404	+	.	Target_ID=356743at4751_653667_1:0010d9;TCS_ID=356743at4751_653667_1:0010d9|snap-NC_003421.2-processed-gene-6.22-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-21.83-mRNA-1	MetaEuk	gene	1	792	411	+	.	Target_ID=362250at4751_653667_1:000af6;TCS_ID=362250at4751_653667_1:000af6|augustus-NC_003421.2-processed-gene-21.83-mRNA-1|+|0
snap-NC_003421.2-processed-gene-9.97-mRNA-1	MetaEuk	gene	7	735	434	+	.	Target_ID=369435at4751_653667_1:0010fd;TCS_ID=369435at4751_653667_1:0010fd|snap-NC_003421.2-processed-gene-9.97-mRNA-1|+|6
maker-NC_003421.2-augustus-gene-9.74-mRNA-1	MetaEuk	gene	304	1119	504	+	.	Target_ID=372972at4751_402676_1:000dbb;TCS_ID=372972at4751_402676_1:000dbb|maker-NC_003421.2-augustus-gene-9.74-mRNA-1|+|303
snap-NC_003421.2-processed-gene-12.21-mRNA-1	MetaEuk	gene	346	2865	551	+	.	Target_ID=37642at4751_483514_1:001272;TCS_ID=37642at4751_483514_1:001272|snap-NC_003421.2-processed-gene-12.21-mRNA-1|+|345
augustus-NC_003421.2-processed-gene-3.53-mRNA-1	MetaEuk	gene	4	1626	628	+	.	Target_ID=378436at4751_653667_1:000ff9;TCS_ID=378436at4751_653667_1:000ff9|augustus-NC_003421.2-processed-gene-3.53-mRNA-1|+|3
snap-NC_003421.2-processed-gene-21.2-mRNA-1	MetaEuk	gene	1	570	340	+	.	Target_ID=379525at4751_483514_1:00015b;TCS_ID=379525at4751_483514_1:00015b|snap-NC_003421.2-processed-gene-21.2-mRNA-1|+|0
snap-NC_003421.2-processed-gene-8.36-mRNA-1	MetaEuk	gene	1	612	391	+	.	Target_ID=385139at4751_653667_1:001005;TCS_ID=385139at4751_653667_1:001005|snap-NC_003421.2-processed-gene-8.36-mRNA-1|+|0
snap-NC_003421.2-processed-gene-22.20-mRNA-1	MetaEuk	gene	1	543	314	+	.	Target_ID=387347at4751_653667_1:000a8c;TCS_ID=387347at4751_653667_1:000a8c|snap-NC_003421.2-processed-gene-22.20-mRNA-1|+|0
maker-NC_003421.2-snap-gene-1.88-mRNA-1	MetaEuk	gene	178	708	295	+	.	Target_ID=387759at4751_653667_1:001031;TCS_ID=387759at4751_653667_1:001031|maker-NC_003421.2-snap-gene-1.88-mRNA-1|+|177
augustus-NC_003421.2-processed-gene-12.39-mRNA-1	MetaEuk	gene	4589	5641	531	+	.	Target_ID=389547at4751_483514_1:0012bb;TCS_ID=389547at4751_483514_1:0012bb|augustus-NC_003421.2-processed-gene-12.39-mRNA-1|+|4588
maker-NC_003421.2-augustus-gene-4.62-mRNA-1	MetaEuk	gene	92	1057	567	+	.	Target_ID=390518at4751_653667_1:0010c6;TCS_ID=390518at4751_653667_1:0010c6|maker-NC_003421.2-augustus-gene-4.62-mRNA-1|+|91
snap-NC_003421.2-processed-gene-17.96-mRNA-1	MetaEuk	gene	1	621	314	+	.	Target_ID=399413at4751_653667_1:0008a0;TCS_ID=399413at4751_653667_1:0008a0|snap-NC_003421.2-processed-gene-17.96-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-9.65-mRNA-1	MetaEuk	gene	26	652	337	+	.	Target_ID=399810at4751_483514_1:000dc5;TCS_ID=399810at4751_483514_1:000dc5|maker-NC_003421.2-augustus-gene-9.65-mRNA-1|+|25
snap-NC_003421.2-processed-gene-11.7-mRNA-1	MetaEuk	gene	28	924	409	+	.	Target_ID=401387at4751_483514_1:0010b5;TCS_ID=401387at4751_483514_1:0010b5|snap-NC_003421.2-processed-gene-11.7-mRNA-1|+|27
maker-NC_003421.2-augustus-gene-22.102-mRNA-1	MetaEuk	gene	159	1013	414	+	.	Target_ID=403079at4751_483514_1:000201;TCS_ID=403079at4751_483514_1:000201|maker-NC_003421.2-augustus-gene-22.102-mRNA-1|+|158
maker-NC_003421.2-augustus-gene-19.47-mRNA-1	MetaEuk	gene	383	1582	520	+	.	Target_ID=407348at4751_653667_1:000c1f;TCS_ID=407348at4751_653667_1:000c1f|maker-NC_003421.2-augustus-gene-19.47-mRNA-1|+|382
snap-NC_003421.2-processed-gene-14.77-mRNA-1	MetaEuk	gene	10	981	557	+	.	Target_ID=410782at4751_653667_1:0009f5;TCS_ID=410782at4751_653667_1:0009f5|snap-NC_003421.2-processed-gene-14.77-mRNA-1|+|9
maker-NC_003421.2-snap-gene-15.45-mRNA-1	MetaEuk	gene	156	758	178	+	.	Target_ID=411130at4751_237631_1:0017a8;TCS_ID=411130at4751_237631_1:0017a8|maker-NC_003421.2-snap-gene-15.45-mRNA-1|+|155
maker-NC_003421.2-augustus-gene-1.96-mRNA-1	MetaEuk	gene	65	604	366	+	.	Target_ID=412006at4751_653667_1:00105b;TCS_ID=412006at4751_653667_1:00105b|maker-NC_003421.2-augustus-gene-1.96-mRNA-1|+|64
snap-NC_003421.2-processed-gene-9.76-mRNA-1	MetaEuk	gene	1	699	418	+	.	Target_ID=419200at4751_653667_1:00115a;TCS_ID=419200at4751_653667_1:00115a|snap-NC_003421.2-processed-gene-9.76-mRNA-1|+|0
maker-NC_003421.2-snap-gene-6.66-mRNA-1	MetaEuk	gene	205	729	255	+	.	Target_ID=419667at4751_653667_1:00111e;TCS_ID=419667at4751_653667_1:00111e|maker-NC_003421.2-snap-gene-6.66-mRNA-1|+|204
maker-NC_003421.2-snap-gene-7.34-mRNA-1	MetaEuk	gene	1836	2375	319	+	.	Target_ID=421097at4751_483514_1:0007c7;TCS_ID=421097at4751_483514_1:0007c7|maker-NC_003421.2-snap-gene-7.34-mRNA-1|+|1835
maker-NC_003421.2-augustus-gene-1.94-mRNA-1	MetaEuk	gene	84	1199	433	+	.	Target_ID=422764at4751_653667_1:0009be;TCS_ID=422764at4751_653667_1:0009be|maker-NC_003421.2-augustus-gene-1.94-mRNA-1|+|83
maker-NC_003421.2-augustus-gene-13.53-mRNA-1	MetaEuk	gene	505	921	280	+	.	Target_ID=423166at4751_483514_1:000e4a;TCS_ID=423166at4751_483514_1:000e4a|maker-NC_003421.2-augustus-gene-13.53-mRNA-1|+|504
snap-NC_003421.2-processed-gene-8.1-mRNA-1	MetaEuk	gene	1	459	273	+	.	Target_ID=428342at4751_653667_1:0010cf;TCS_ID=428342at4751_653667_1:0010cf|snap-NC_003421.2-processed-gene-8.1-mRNA-1|+|0
snap-NC_003421.2-processed-gene-22.32-mRNA-1	MetaEuk	gene	22	582	213	+	.	Target_ID=433384at4751_483514_1:000619;TCS_ID=433384at4751_483514_1:000619|snap-NC_003421.2-processed-gene-22.32-mRNA-1|+|21
snap-NC_003421.2-processed-gene-13.100-mRNA-1	MetaEuk	gene	1	570	224	+	.	Target_ID=444602at4751_653667_1:0008e0;TCS_ID=444602at4751_653667_1:0008e0|snap-NC_003421.2-processed-gene-13.100-mRNA-1|+|0
maker-NC_003421.2-snap-gene-7.44-mRNA-1	MetaEuk	gene	96	521	222	+	.	Target_ID=445954at4751_483514_1:000b1c;TCS_ID=445954at4751_483514_1:000b1c|maker-NC_003421.2-snap-gene-7.44-mRNA-1|+|95
maker-NC_003421.2-augustus-gene-14.60-mRNA-1	MetaEuk	gene	200	880	396	+	.	Target_ID=449717at4751_653667_1:0009c2;TCS_ID=449717at4751_653667_1:0009c2|maker-NC_003421.2-augustus-gene-14.60-mRNA-1|+|199
augustus-NC_003421.2-processed-gene-7.11-mRNA-1	MetaEuk	gene	245	946	274	+	.	Target_ID=449803at4751_653667_1:001145;TCS_ID=449803at4751_653667_1:001145|augustus-NC_003421.2-processed-gene-7.11-mRNA-1|+|244
snap-NC_003421.2-processed-gene-11.9-mRNA-1	MetaEuk	gene	55	792	334	+	.	Target_ID=454840at4751_653667_1:000c80;TCS_ID=454840at4751_653667_1:000c80|snap-NC_003421.2-processed-gene-11.9-mRNA-1|+|54
augustus-NC_003421.2-processed-gene-21.98-mRNA-1	MetaEuk	gene	1	1002	368	+	.	Target_ID=458980at4751_653667_1:000bec;TCS_ID=458980at4751_653667_1:000bec|augustus-NC_003421.2-processed-gene-21.98-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-22.105-mRNA-1	MetaEuk	gene	160	684	307	+	.	Target_ID=459844at4751_653667_1:000a84;TCS_ID=459844at4751_653667_1:000a84|maker-NC_003421.2-augustus-gene-22.105-mRNA-1|+|159
maker-NC_003421.2-augustus-gene-3.1-mRNA-1	MetaEuk	gene	79	3078	1535	+	.	Target_ID=46098at4751_653667_1:000fef;TCS_ID=46098at4751_653667_1:000fef|maker-NC_003421.2-augustus-gene-3.1-mRNA-1|+|78
snap-NC_003421.2-processed-gene-9.78-mRNA-1	MetaEuk	gene	1	624	341	+	.	Target_ID=464711at4751_653667_1:0010d7;TCS_ID=464711at4751_653667_1:0010d7|snap-NC_003421.2-processed-gene-9.78-mRNA-1|+|0
snap-NC_003421.2-processed-gene-21.39-mRNA-1	MetaEuk	gene	1	1005	261	+	.	Target_ID=474125at4751_653667_1:000b29;TCS_ID=474125at4751_653667_1:000b29|snap-NC_003421.2-processed-gene-21.39-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-21.86-mRNA-1	MetaEuk	gene	70	453	244	+	.	Target_ID=474374at4751_653667_1:000c1d;TCS_ID=474374at4751_653667_1:000c1d|augustus-NC_003421.2-processed-gene-21.86-mRNA-1|+|69
maker-NC_003421.2-snap-gene-21.69-mRNA-1	MetaEuk	gene	121	1023	345	+	.	Target_ID=482337at4751_653667_1:000c60;TCS_ID=482337at4751_653667_1:000c60|maker-NC_003421.2-snap-gene-21.69-mRNA-1|+|120
maker-NC_003421.2-augustus-gene-11.45-mRNA-1	MetaEuk	gene	62	580	186	+	.	Target_ID=485650at4751_483514_1:000dfb;TCS_ID=485650at4751_483514_1:000dfb|maker-NC_003421.2-augustus-gene-11.45-mRNA-1|+|61
maker-NC_003421.2-snap-gene-6.72-mRNA-1	MetaEuk	gene	1	387	182	+	.	Target_ID=490662at4751_653667_1:001012;TCS_ID=490662at4751_653667_1:001012|maker-NC_003421.2-snap-gene-6.72-mRNA-1|+|0
snap-NC_003421.2-processed-gene-19.64-mRNA-1	MetaEuk	gene	1	14151	5082	+	.	Target_ID=494at4751_653667_1:000b57;TCS_ID=494at4751_653667_1:000b57|snap-NC_003421.2-processed-gene-19.64-mRNA-1|+|0
snap-NC_003421.2-processed-gene-12.13-mRNA-1	MetaEuk	gene	178	3867	1647	+	.	Target_ID=58127at4751_653667_1:000d01;TCS_ID=58127at4751_653667_1:000d01|snap-NC_003421.2-processed-gene-12.13-mRNA-1|+|177
maker-NC_003421.2-augustus-gene-22.99-mRNA-1	MetaEuk	gene	211	2910	1286	+	.	Target_ID=61438at4751_483514_1:0001db;TCS_ID=61438at4751_483514_1:0001db|maker-NC_003421.2-augustus-gene-22.99-mRNA-1|+|210
maker-NC_003421.2-augustus-gene-6.53-mRNA-1	MetaEuk	gene	117	2045	1059	+	.	Target_ID=65334at4751_483514_1:000920;TCS_ID=65334at4751_483514_1:000920|maker-NC_003421.2-augustus-gene-6.53-mRNA-1|+|116
snap-NC_003421.2-processed-gene-23.20-mRNA-1	MetaEuk	gene	1	2505	1125	+	.	Target_ID=65499at4751_653667_1:000b7a;TCS_ID=65499at4751_653667_1:000b7a|snap-NC_003421.2-processed-gene-23.20-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-13.58-mRNA-1	MetaEuk	gene	522	2678	1025	+	.	Target_ID=66151at4751_653667_1:00087c;TCS_ID=66151at4751_653667_1:00087c|maker-NC_003421.2-augustus-gene-13.58-mRNA-1|+|521
maker-NC_003421.2-augustus-gene-3.16-mRNA-1	MetaEuk	gene	226	2325	1214	+	.	Target_ID=67399at4751_653667_1:001114;TCS_ID=67399at4751_653667_1:001114|maker-NC_003421.2-augustus-gene-3.16-mRNA-1|+|225
maker-NC_003421.2-augustus-gene-16.101-mRNA-1	MetaEuk	gene	222	2606	1189	+	.	Target_ID=71046at4751_653667_1:000af4;TCS_ID=71046at4751_653667_1:000af4|maker-NC_003421.2-augustus-gene-16.101-mRNA-1|+|221
maker-NC_003421.2-augustus-gene-11.47-mRNA-1	MetaEuk	gene	1	3948	1940	+	.	Target_ID=75709at4751_653667_1:000d74;TCS_ID=75709at4751_653667_1:000d74|maker-NC_003421.2-augustus-gene-11.47-mRNA-1|+|0
snap-NC_003421.2-processed-gene-9.112-mRNA-1	MetaEuk	gene	1	1755	1067	+	.	Target_ID=79294at4751_483514_1:001102;TCS_ID=79294at4751_483514_1:001102|snap-NC_003421.2-processed-gene-9.112-mRNA-1|+|0
augustus-NC_003421.2-processed-gene-8.75-mRNA-1	MetaEuk	gene	1	2331	1223	+	.	Target_ID=79797at4751_483514_1:000aaa;TCS_ID=79797at4751_483514_1:000aaa|augustus-NC_003421.2-processed-gene-8.75-mRNA-1|+|0
maker-NC_003421.2-augustus-gene-21.51-mRNA-1	MetaEuk	gene	204	2411	676	+	.	Target_ID=79988at4751_653667_1:000bf1;TCS_ID=79988at4751_653667_1:000bf1|maker-NC_003421.2-augustus-gene-21.51-mRNA-1|+|203
snap-NC_003421.2-processed-gene-6.6-mRNA-1	MetaEuk	gene	1	5052	2277	+	.	Target_ID=81614at4751_653667_1:00109f;TCS_ID=81614at4751_653667_1:00109f|snap-NC_003421.2-processed-gene-6.6-mRNA-1|+|0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genome sequence:
- step_state: scheduled
Step 2: Genome assembly:
- step_state: scheduled

Step 11: Map annotation ids:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_97ca84e4-a0f2-4f87-9407-2d9484e00683.dat' && maker_map_ids --prefix 'TEST_' --justify 6 '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' > '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_3c0f8748-863d-446f-ac8c-aafcddc2c395.dat' && map_gff_ids '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_3c0f8748-863d-446f-ac8c-aafcddc2c395.dat' '/tmp/tmp9cvtqig0/job_working_directory/000/11/outputs/dataset_97ca84e4-a0f2-4f87-9407-2d9484e00683.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
justify	`"6"`
prefix	`"TEST_"`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp9cvtqig0/files/9/3/2/dataset_93278d3b-41ee-48e7-908b-e13196d0f653.dat' --mode 'tran' --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 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-18 14:45:08 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
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:

2024-12-18 14:37:45 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/18/2024 14:37:45 *****
2024-12-18 14:37:45 INFO:	Configuring BUSCO with local environment
2024-12-18 14:37:45 INFO:	Running transcriptome mode
2024-12-18 14:37:45 INFO:	Input file is /tmp/tmp9cvtqig0/files/9/3/2/dataset_93278d3b-41ee-48e7-908b-e13196d0f653.dat
2024-12-18 14:37:45 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2024-12-18 14:37:45 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:37:45
2024-12-18 14:40:26 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:40:26 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:40:26 INFO:	Running 758 job(s) on hmmsearch, starting at 12/18/2024 14:40:26
2024-12-18 14:40:29 INFO:	[hmmsearch]	76 of 758 task(s) completed
2024-12-18 14:40:30 INFO:	[hmmsearch]	152 of 758 task(s) completed
2024-12-18 14:40:32 INFO:	[hmmsearch]	228 of 758 task(s) completed
2024-12-18 14:40:34 INFO:	[hmmsearch]	304 of 758 task(s) completed
2024-12-18 14:40:35 INFO:	[hmmsearch]	379 of 758 task(s) completed
2024-12-18 14:40:36 INFO:	[hmmsearch]	455 of 758 task(s) completed
2024-12-18 14:40:37 INFO:	[hmmsearch]	531 of 758 task(s) completed
2024-12-18 14:40:38 INFO:	[hmmsearch]	607 of 758 task(s) completed
2024-12-18 14:40:39 INFO:	[hmmsearch]	683 of 758 task(s) completed
2024-12-18 14:40:41 INFO:	[hmmsearch]	758 of 758 task(s) completed
2024-12-18 14:40:41 INFO:	140 exons in total
2024-12-18 14:40:41 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-12-18 14:41:02 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:41:02
2024-12-18 14:44:53 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:44:53 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:44:53 INFO:	Running 630 job(s) on hmmsearch, starting at 12/18/2024 14:44:53
2024-12-18 14:44:55 INFO:	[hmmsearch]	63 of 630 task(s) completed
2024-12-18 14:44:56 INFO:	[hmmsearch]	126 of 630 task(s) completed
2024-12-18 14:44:57 INFO:	[hmmsearch]	189 of 630 task(s) completed
2024-12-18 14:44:58 INFO:	[hmmsearch]	252 of 630 task(s) completed
2024-12-18 14:44:59 INFO:	[hmmsearch]	315 of 630 task(s) completed
2024-12-18 14:45:00 INFO:	[hmmsearch]	378 of 630 task(s) completed
2024-12-18 14:45:01 INFO:	[hmmsearch]	441 of 630 task(s) completed
2024-12-18 14:45:02 INFO:	[hmmsearch]	504 of 630 task(s) completed
2024-12-18 14:45:03 INFO:	[hmmsearch]	567 of 630 task(s) completed
2024-12-18 14:45:04 INFO:	[hmmsearch]	630 of 630 task(s) completed
2024-12-18 14:45:05 INFO:	1 candidate overlapping regions found
2024-12-18 14:45:05 INFO:	143 exons in total
2024-12-18 14:45:05 INFO:	Results:	C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758	   

2024-12-18 14:45:05 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.8%,D:0.1%],F:1.5%,M:81.6%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |127    Complete and single-copy BUSCOs (S)        |
    |1    Complete and duplicated BUSCOs (D)           |
    |11    Fragmented BUSCOs (F)                       |
    |619    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-12-18 14:45:05 INFO:	BUSCO analysis done with WARNING(s). Total running time: 440 seconds

***** Summary of warnings: *****
2024-12-18 14:37:45 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:37:45 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2024-12-18 14:45:05 INFO:	Results written in /tmp/tmp9cvtqig0/job_working_directory/000/12/working/busco_galaxy
2024-12-18 14:45:05 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-18 14:45:05 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 64
drwxr-xr-x 5 1001 118  4096 Dec 18 14:37 busco_sequences
-rw-r--r-- 1 1001 118 36033 Dec 18 14:45 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Dec 18 14:40 hmmer_output
drwxr-xr-x 4 1001 118  4096 Dec 18 14:45 metaeuk_output
-rw-r--r-- 1 1001 118  8066 Dec 18 14:45 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2395 Dec 18 14:45 short_summary.json
-rw-r--r-- 1 1001 118   761 Dec 18 14:45 short_summary.txt
2024-12-18 14:45:06 INFO:	****************** Start plot generation at 12/18/2024 14:45:06 ******************
2024-12-18 14:45:06 INFO:	Load data ...
2024-12-18 14:45:06 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2024-12-18 14:45:06 INFO:	Generate the R code ...
2024-12-18 14:45:06 INFO:	Run the R code ...
2024-12-18 14:45:08 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-18 14:45:08 INFO:	Plot generation done. Total running time: 2.167381525039673 seconds
2024-12-18 14:45:08 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files &&  cp /tmp/tmp9cvtqig0/job_working_directory/000/13/configs/tmpzlqn969i /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_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/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files /tmp/tmp9cvtqig0/job_working_directory/000/13/configs/tmpzlqn969i &&  cp /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7_files/index.html /tmp/tmp9cvtqig0/job_working_directory/000/13/outputs/dataset_fd23a98e-ab40-4e23-ae8d-f9fc83c80cb7.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Maker annotation / Map annotation ids on data 12: renamed GFF
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__	`"15171aa2bd4a11ef8af66045bd0269f9"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp9cvtqig0/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": "Maker annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 18, "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_off"}}]}]
uglyTestingHack	`""`

Step 3: Protein sequences:
- step_state: scheduled
Step 4: Augustus training:
- step_state: scheduled
Step 5: SNAP training:
- step_state: scheduled

**Step 6: Fasta Statistics **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' --stats_output '/tmp/tmp9cvtqig0/job_working_directory/000/6/outputs/dataset_e8e5918e-83c5-4043-b6e9-a0061e7cbbbe.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' --mode 'tran' --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 'fungi_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-18 14:24:55 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
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:

2024-12-18 14:14:03 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 12/18/2024 14:14:03 *****
2024-12-18 14:14:03 INFO:	Configuring BUSCO with local environment
2024-12-18 14:14:03 INFO:	Running transcriptome mode
2024-12-18 14:14:05 INFO:	Input file is /tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat
2024-12-18 14:14:05 WARNING:	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 INFO:	Running BUSCO using lineage dataset fungi_odb10 (eukaryota, 2021-06-28)
2024-12-18 14:14:05 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:14:05
2024-12-18 14:17:18 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:17:18 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:17:18 INFO:	Running 758 job(s) on hmmsearch, starting at 12/18/2024 14:17:18
2024-12-18 14:17:26 INFO:	[hmmsearch]	76 of 758 task(s) completed
2024-12-18 14:17:33 INFO:	[hmmsearch]	152 of 758 task(s) completed
2024-12-18 14:17:40 INFO:	[hmmsearch]	228 of 758 task(s) completed
2024-12-18 14:17:47 INFO:	[hmmsearch]	304 of 758 task(s) completed
2024-12-18 14:17:53 INFO:	[hmmsearch]	379 of 758 task(s) completed
2024-12-18 14:17:59 INFO:	[hmmsearch]	455 of 758 task(s) completed
2024-12-18 14:18:05 INFO:	[hmmsearch]	531 of 758 task(s) completed
2024-12-18 14:18:11 INFO:	[hmmsearch]	607 of 758 task(s) completed
2024-12-18 14:18:17 INFO:	[hmmsearch]	683 of 758 task(s) completed
2024-12-18 14:18:24 INFO:	[hmmsearch]	758 of 758 task(s) completed
2024-12-18 14:18:24 INFO:	1 candidate overlapping regions found
2024-12-18 14:18:24 INFO:	265 exons in total
2024-12-18 14:18:25 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2024-12-18 14:18:46 INFO:	Running 1 job(s) on metaeuk, starting at 12/18/2024 14:18:46
2024-12-18 14:24:40 INFO:	[metaeuk]	1 of 1 task(s) completed
2024-12-18 14:24:40 INFO:	***** Run HMMER on gene sequences *****
2024-12-18 14:24:40 INFO:	Running 630 job(s) on hmmsearch, starting at 12/18/2024 14:24:40
2024-12-18 14:24:42 INFO:	[hmmsearch]	63 of 630 task(s) completed
2024-12-18 14:24:43 INFO:	[hmmsearch]	126 of 630 task(s) completed
2024-12-18 14:24:44 INFO:	[hmmsearch]	189 of 630 task(s) completed
2024-12-18 14:24:45 INFO:	[hmmsearch]	252 of 630 task(s) completed
2024-12-18 14:24:46 INFO:	[hmmsearch]	315 of 630 task(s) completed
2024-12-18 14:24:47 INFO:	[hmmsearch]	378 of 630 task(s) completed
2024-12-18 14:24:48 INFO:	[hmmsearch]	441 of 630 task(s) completed
2024-12-18 14:24:49 INFO:	[hmmsearch]	504 of 630 task(s) completed
2024-12-18 14:24:50 INFO:	[hmmsearch]	567 of 630 task(s) completed
2024-12-18 14:24:51 INFO:	[hmmsearch]	630 of 630 task(s) completed
2024-12-18 14:24:52 INFO:	5 candidate overlapping regions found
2024-12-18 14:24:52 INFO:	273 exons in total
2024-12-18 14:24:52 INFO:	Results:	C:16.9%[S:16.9%,D:0.0%],F:1.3%,M:81.8%,n:758	   

2024-12-18 14:24:52 INFO:	

    ---------------------------------------------------
    |Results from dataset fungi_odb10                  |
    ---------------------------------------------------
    |C:16.9%[S:16.9%,D:0.0%],F:1.3%,M:81.8%,n:758      |
    |128    Complete BUSCOs (C)                        |
    |128    Complete and single-copy BUSCOs (S)        |
    |0    Complete and duplicated BUSCOs (D)           |
    |10    Fragmented BUSCOs (F)                       |
    |620    Missing BUSCOs (M)                         |
    |758    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-12-18 14:24:52 INFO:	BUSCO analysis done with WARNING(s). Total running time: 647 seconds

***** Summary of warnings: *****
2024-12-18 14:14:05 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2024-12-18 14:14:05 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2024-12-18 14:24:52 INFO:	Results written in /tmp/tmp9cvtqig0/job_working_directory/000/7/working/busco_galaxy
2024-12-18 14:24:52 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-18 14:24:52 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 60
drwxr-xr-x 5 1001 118  4096 Dec 18 14:14 busco_sequences
-rw-r--r-- 1 1001 118 32181 Dec 18 14:24 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Dec 18 14:18 hmmer_output
drwxr-xr-x 4 1001 118  4096 Dec 18 14:24 metaeuk_output
-rw-r--r-- 1 1001 118  8079 Dec 18 14:24 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2393 Dec 18 14:24 short_summary.json
-rw-r--r-- 1 1001 118   761 Dec 18 14:24 short_summary.txt
2024-12-18 14:24:53 INFO:	****************** Start plot generation at 12/18/2024 14:24:53 ******************
2024-12-18 14:24:53 INFO:	Load data ...
2024-12-18 14:24:53 INFO:	Loaded BUSCO_summaries/short_summary.specific.fungi_odb10.busco_galaxy.txt successfully
2024-12-18 14:24:53 INFO:	Generate the R code ...
2024-12-18 14:24:53 INFO:	Run the R code ...
2024-12-18 14:24:55 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-18 14:24:55 INFO:	Plot generation done. Total running time: 2.2214157581329346 seconds
2024-12-18 14:24:55 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "fungi_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: Maker:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi &&  LIBDIR=$(dirname "$RM_PATH")/../share/RepeatMasker/Libraries &&  export LIBDIR &&  maker -CTL  &&  cp '/tmp/tmp9cvtqig0/job_working_directory/000/8/configs/tmp0heb0krf' maker_opts.ctl  &&    cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&  mkdir -p 'augustus_dir/species/' &&  tar -C 'augustus_dir/species/' -xzvf '/tmp/tmp9cvtqig0/files/9/8/2/dataset_982d13e6-6f2c-4fb1-9ee6-7f668291f94e.dat' > /dev/null &&  export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  MPI_CMD="" && if [ "$MAKER_MPI" == "1" ]; then MPI_CMD="mpiexec -n ${GALAXY_SLOTS:-4}"; fi &&  ${MPI_CMD} maker --ignore_nfs_tmp  maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null  &&  gff3_merge -d *.maker.output/*_master_datastore_index.log -o '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_8a2dba4b-91ab-451a-8041-524f850cb4c8.dat'  &&  awk '{if ($2 == "maker" || $1 ~ /^#/) {print}}' '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_8a2dba4b-91ab-451a-8041-524f850cb4c8.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat'  &&  awk '{if ($2 != "maker") {print}}' '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_8a2dba4b-91ab-451a-8041-524f850cb4c8.dat' | sed -n '/^##FASTA$/q;p' > '/tmp/tmp9cvtqig0/job_working_directory/000/8/outputs/dataset_20ce8a00-e1f3-449d-a8c1-cb8d901133b1.dat'

Exit Code:

```
0
```

Standard Error:

Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore

To access files for individual sequences use the datastore index:
/tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: NC_003421.2
Length: 2452883
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e%2Edat.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --UTR=off /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/NC_003421%2E2.abinit_nomask.0.local.augustus
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.0 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.0.blastn
#-------------------------------#
deleted:2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.1 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.1.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.2
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.2 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.2.blastn
#-------------------------------#
deleted:1 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.3
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.3 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.3.blastn
#-------------------------------#
deleted:0 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.4
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.4 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.4.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.5
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.5 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.5.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.6
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.6 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.6.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.7
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.7 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.7.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.8 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.8.blastn
#-------------------------------#
deleted:-2 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype nucl -in /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/blastprep/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/local/bin/blastn -db /tmp/tmp9cvtqig0/tmp/maker_cn677n/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.9 -query /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking false -show_gis -out /tmp/tmp9cvtqig0/job_working_directory/000/8/working/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.maker.output/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a_datastore/0B/63/NC_003421.2//theVoid.NC_003421.2/0/NC_003421%2E2.0.dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.blastn.temp_dir/dataset_e778a466-b99c-43bc-b589-ecd28de82e1e%2Edat.mpi.10.9.blastn
#-------------------------------#
deleted:-1 hits
collecting blastn reports
in cluster::shadow_cluster...
...finished clustering.
polishig ESTs
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g1_i1.for.1209-2601.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2601.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2601.TRINITY_DN2776_c0_g1_i1.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g1_i2.for.1417-2601.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1417-2601.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1417-2601.TRINITY_DN2776_c0_g1_i2.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g3_i1.for.1209-2201.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2201.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1209-2201.TRINITY_DN2776_c0_g3_i1.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g1_i3.for.1451-2601.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1451-2601.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1451-2601.TRINITY_DN2776_c0_g1_i3.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate::est2genome:
/usr/local/bin/exonerate  -q /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/TRINITY_DN2776_c0_g2_i1.for.1962-3582.0.fasta -t /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1962-3582.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/NC_003421%2E2.1962-3582.TRINITY_DN2776_c0_g2_i1.e.exonerate
#-------------------------------#
running  est2genome search.
#--------- command -------------#
Widget::exonerate:
..
2-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/132_0.2303936-2305950.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/133_0.2317785-2319394.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/134_0.2326855-2328897.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/135_0.2329261-2334928.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/136_0.2341240-2344143.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/137_0.2349164-2354609.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/138_0.2366363-2370156.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/139_0.2373919-2380223.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/140_0.2381056-2382231.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/141_0.2384415-2388063.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/142_0.2388096-2391775.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/143_0.2407535-2408933.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /tmp/tmp9cvtqig0/files/0/b/d/dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat -xdef /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.xdef.snap  /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.dataset_0bd40b92-e223-4bee-a43a-e8a312bd586e.dat.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/bin/augustus --species=local --strand=backward --UTR=off --hintsfile=/tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.local.auto_annotator.xdef.augustus --extrinsicCfgFile=/tmp/tmp9cvtqig0/job_working_directory/000/8/working/augustus_dir//extrinsic/extrinsic.MPE.cfg /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.local.auto_annotator.augustus.fasta > /tmp/tmp9cvtqig0/tmp/maker_cn677n/0/144_0.2428734-2431724.local.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output


Maker is now finished!!!

Standard Output:

Start_time: 1734531234
End_time:   1734532644
Elapsed:    1410

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
abinitio_gene_prediction	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 4, "src": "hda"}]}}, "snaphmm": {"values": [{"id": 5, "src": "hda"}]}, "unmask": false}`
advanced	`{"AED_threshold": "1.0", "alt_peptide": "C", "alt_splice": false, "always_complete": false, "correct_est_fusion": false, "fix_nucleotides": false, "keep_preds": "0.0", "map_forward": false, "max_dna_len": "100000", "min_contig": "1", "min_protein": "0", "other_gff": null, "pred_flank": "200", "pred_stats": false, "single_exon": {"__current_case__": 0, "single_exon": "0"}, "split_hit": "10000"}`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
est_evidences	`{"altest": null, "altest_gff": null, "est": {"values": [{"id": 2, "src": "hda"}]}, "est2genome": false, "est_gff": null}`
gene_prediction	`{"model_gff": null, "pred_gff": null, "snoscan_rrna": null, "trna": false}`
license_agreement	`true`
organism_type	`"eukaryotic"`
protein_evidences	`{"protein": {"values": [{"id": 3, "src": "hda"}]}, "protein2genome": false, "protein_gff": null}`
reannotation	`{"__current_case__": 0, "reannotate": "no"}`
repeat_masking	`{"repeat_source": {"__current_case__": 3, "source_type": "no"}}`

Step 9: GFFRead:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' genomeref.fa &&  gffread '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' -g genomeref.fa  -F -D -E  -w exons.fa

Exit Code:

```
0
```

Standard Error:

Command line was:
gffread /tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat -g genomeref.fa -F -D -E -w exons.fa
FASTA index file genomeref.fa.fai created.
   .. loaded 864 genomic features from /tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chr_replace	`None`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`true`
expose	`true`
filtering	`None`
full_gff_attribute_preservation	`true`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-w exons.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 10: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9cvtqig0/files/d/9/c/dataset_d9c4d846-db8e-43a8-89de-8574688002a8.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_753f9010-5b18-4355-955e-39c082dc5a54.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp9cvtqig0/files/d/6/1/dataset_d6104160-242f-4c1b-a7b9-8ca1b3e4652a.dat' 2>&1 | tail -n +3 >> '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_753f9010-5b18-4355-955e-39c082dc5a54.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_753f9010-5b18-4355-955e-39c082dc5a54.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp9cvtqig0/job_working_directory/000/10/outputs/dataset_1894acd3-9681-47ef-a814-19f0303449f3.dat'

Exit Code:

```
0
```

Standard Error:

�[0;33m14:38:07 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Imported 864 records from `transcript.sizes`.�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m14:38:09 [base]�[0m�[0;35m Imported 864 records from `transcript.sizes`.�[0m
�[0;33m14:38:09 [stats]�[0m�[0;35m A total of 864 transcripts populated.�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m platform is linux2�[0m
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'unittest.suite', '_ctypes', 'xml.etree', 'json.scanner', 'codecs', 'Bio.collections', 'numpy.os', 'jcvi.annotation.jcvi', 'mkl_fft._numpy_fft', 'StringIO', 'Bio.Alphabet.IUPAC', 'weakref', 'numpy.core._internal', 'distutils.sys', 'numpy.lib.arraypad', 'pprint', 'Bio.SeqIO.math', 'Bio.warnings', 'jcvi.apps.httplib', 'sqlite3.dbapi2', 'select', 'ctypes._ctypes', '_heapq', 'six.moves.urllib', 'numpy.lib.financial', 'Bio.Align.Generic', 'binascii', 'jcvi.formats.sizes', 'unittest.loader', 'unittest.fnmatch', 'numpy.polynomial.chebyshev', '_functools', 'cPickle', 'numpy.polynomial.hermite_e', 'jcvi.apps.urllib', 'jcvi', 'numpy.testing.utils', 'jcvi.graphics.histogram', 'jcvi.utils.UserDict', 'numpy.core.fromnumeric', 'unicodedata', 'numpy.ctypeslib', 'matplotlib._version', '_ast', 'jcvi.utils.range', 'encodings.aliases', 'Bio.SeqIO.SeqXmlIO', 'fnmatch', 'sre_parse', 'pickle', 'Bio.SeqIO.AceIO', 'numpy.random.warnings', 'xml.sax.types', 'jcvi.utils.itertools', 'logging.cStringIO', 'Bio.SeqIO.os', 'numpy.lib.polynomial', 'numpy.compat', 'numbers', 'numpy.core.records', 'strop', 'xml.etree.ElementPath', 'numpy.core.numeric', 'six', 'Bio.array', 'jcvi.apps', 'matplotlib.testing', 'Bio.Alphabet.Bio', 'numpy.lib.utils', 'numpy.lib.arrayterator', 'os.path', 'Bio.GenBank.__future__', '_weakrefset', 'Bio.SeqIO.warnings', 'unittest.traceback', 'unittest.os', 'jcvi.utils.table', 'functools', 'sysconfig', 'sqlite3.collections', 'numpy.polynomial.legendre', 'numpy.matrixlib.defmatrix', 'tempfile', 'imp', 'jcvi.apps.subprocess', 'jcvi.formats.urllib', 'Bio._py3k.commands', 'Bio.SeqIO.Interfaces', 'numpy.linalg.info', 'jcvi.utils.re', 'jcvi.formats.Bio', 'xml.etree._elementtree', 'unittest.util', 'Bio.SeqIO.struct', 'jcvi.apps.time', 'httplib', 'decimal', 'numpy.lib._datasource', 'Bio._py3k.__builtin__', 'jcvi.formats.os', 'jcvi.apps.unicodedata', 'numpy.linalg._umath_linalg', 'cStringIO', 'numpy.polynomial', 'jcvi.annotation.reformat', 'jcvi.graphics.sys', 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'logging.traceback', 'numpy.matrixlib', 'Bio.SeqIO.xml', 'numpy.testing.nose_tools.decorators', 'token', 'backports', 'numpy.lib.mixins', '_posixsubprocess32', 'Bio.SeqIO', 'glob', 'Bio.GenBank.Scanner', 'mpl_toolkits', 'jcvi.utils.sys', 'UserDict', 'inspect', 'jcvi.utils.bisect', 'logging.sys', 'Bio.SeqIO.collections', 'Bio.itertools', 'Bio.Sequencing.__future__', 'Bio.SeqUtils.CheckSum', 'socket', 'numpy.core.memmap', 'cython_runtime', 'Bio.Align.__future__', 'numpy.linalg.lapack_lite', 'Bio.Seq', 'os', 'marshal', '__future__', 'Bio.Alphabet', 'numpy.core.shape_base', 'jcvi.apps.errno', 'matplotlib.compat', '__builtin__', 'xml.sax.xmlreader', 'operator', 'xml.dom.pulldom', 'distutils.string', 'Bio.GenBank.re', 'jcvi.apps.optparse', 'errno', '_socket', 'json', 'jcvi.apps.shutil', 'Bio.SeqIO.PdbIO', 'xml.sax.handler', 'numpy.testing.nose_tools.utils', 'jcvi.formats.hashlib', 'jcvi.utils.urlparse', '_warnings', 'encodings.__builtin__', 'tokenize', 'numpy._distributor_init', 'pwd', 'numpy.core.getlimits', '_sysconfigdata', 'Bio.SeqIO.SffIO', 'numpy.fft', 'numpy.random.numpy', 'logging.time', 'Bio.GenBank.collections', 'jcvi.formats.gff', 'numpy.lib.function_base', 'logging.warnings', 'mimetools', 'xml.sax', 'Bio._py3k.cStringIO', 'logging.codecs', 'numpy.compat.py3k', 'Bio.Data.CodonTable', 'numpy.polynomial._polybase', 'numpy.polynomial.hermite', 'contextlib', 'numpy.polynomial.polynomial', 'grp', 'numpy.core.defchararray', 'gettext', '_abcoll', 'Bio.SeqFeature', 'xml.sax._exceptions', 'genericpath', 'stat', 'urllib2', 'unittest.signals', 'backports.functools_lru_cache', 'ctypes.ctypes', 'numpy.lib.format', 'numpy.testing.nosetester', 'xml.dom', 'time', 'jcvi.apps.socket', 'jcvi.annotation.os', 'Bio.Sequencing.Ace']�[0m
�[0;33m14:38:10 [__init__]�[0m�[0;35m CACHEDIR=/tmp/tmp9cvtqig0/tmp/matplotlib-KOboYv�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m font search path ['/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf', '/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm', '/usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts']�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono-Oblique.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans-Oblique.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansDisplay.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSansMono.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmr10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizFourSymReg.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymReg.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymBol.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralBolIta.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmtt10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizTwoSymBol.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneral.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmmi10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizOneSymBol.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmb10.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXSizThreeSymReg.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXNonUniIta.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/STIXGeneralItalic.ttf�[0m
�[0;33m14:38:10 [font_manager]�[0m�[0;35m trying fontname /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf/cmss10.ttf�[0m
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Warning message:
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Saving 7 x 7 in image
Warning message:
Removed 428 rows containing non-finite values (stat_bin). 
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Warning message:
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Warning message:
Removed 4 rows containing non-finite values (stat_bin). 
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Gene_Length/input.txt: Min=42 Max=14154 N=864 Mean=1419.35763889 SD=1121.07450652 Median=1108.5 Sum=1226325
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Warning message:
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Saving 7 x 7 in image
Warning message:
Removed 28 rows containing non-finite values (stat_bin). 
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Saving 7 x 7 in image

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"15171aa2bd4a11ef8af66045bd0269f9"`
chromInfo	`"/tmp/tmp9cvtqig0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Other invocation details
- history_id
  - 5319e1fa34219f11
- history_state
  - ok
- invocation_id
  - 5319e1fa34219f11
- invocation_state
  - scheduled
- workflow_id
  - 5319e1fa34219f11

add workflow: annotation a genome with maker

1ce1f00

rlibouba marked this pull request as draft December 11, 2024 09:40

rlibouba changed the title ~~Add workflow: annotation a genome with Maker~~ Add workflow: genome annotation with Maker Dec 11, 2024

Merge branch 'galaxyproject:main' into add_wf_annotation_maker

60b9c0b

wm75 reviewed Dec 12, 2024

View reviewed changes

rlibouba added 2 commits December 17, 2024 15:10

some modification

356d164

error typo

364eb9f

correct error

89c0035

correct error

38d88ae

rlibouba and others added 2 commits December 18, 2024 12:03

correct error

e617648

Merge branch 'galaxyproject:main' into add_wf_annotation_maker

da361e7

Update Genome_annotation_with_maker_short_tests.yml

bc44bb9

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Add workflow: genome annotation with Maker #631

Add workflow: genome annotation with Maker #631

rlibouba commented Dec 11, 2024

wm75 commented Dec 12, 2024

wm75 Dec 12, 2024

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github-actions bot commented Dec 18, 2024

github-actions bot commented Dec 18, 2024

github-actions bot commented Dec 18, 2024

Workflow invocation details

Add workflow: genome annotation with Maker #631

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Add workflow: genome annotation with Maker #631

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github-actions bot commented Dec 18, 2024

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github-actions bot commented Dec 18, 2024

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github-actions bot commented Dec 18, 2024

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Workflow invocation details