funannotate predict errors

[liuyca1]

Are you using the latest release?
funannotate v1.8.17

Describe the bug
When I run funannotate predict I get an error
[Oct 15 05:17 PM]: Training Augustus using BUSCO gene models
Error: In sequence AgBi.1_256224-258221: One CDS exon does not begin properly after the previous CDS exon.1397 >= 1395
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.1_564660-571196: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
。。。

What command did you issue?
$funannotate predict -i Genomic_masked2.fna --species "Agaricus bisporus" -o ./fun --busco_seed_species anidulans --busco_db dikarya --min_training_models 150 --cpus 80 --name AgBi_

Logfiles
$funannotate predict -i Genomic_masked2.fna --species "Agaricus bisporus" -o ./fun --busco_seed_species anidulans --busco_db dikarya --min_training_models 150 --cpus 80 --name AgBi_

[Oct 15 04:47 PM]: OS: CentOS Linux 7, 80 cores, ~ 1584 GB RAM. Python: 3.8.19
[Oct 15 04:47 PM]: Running funannotate v1.8.17
[Oct 15 04:47 PM]: Skipping CodingQuarry as no --rna_bam passed
[Oct 15 04:47 PM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus busco
genemark selftraining
glimmerhmm busco
snap busco
[Oct 15 04:47 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Oct 15 04:47 PM]: Genome loaded: 18 scaffolds; 30,069,126 bp; 10.20% repeats masked
/public/home/liuyuanchao/software/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-p2g.py:14: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import parse_version
[Oct 15 04:47 PM]: Mapping 559,318 proteins to genome using diamond and exonerate
[Oct 15 04:50 PM]: Found 200,093 preliminary alignments with diamond in 0:00:57 --> generated FASTA files for exonerate in 0:01:44
Progress: 200093 complete, 0 failed, 0 remaining
[Oct 15 04:57 PM]: Exonerate finished in 0:06:30: found 739 alignments
[Oct 15 04:57 PM]: Running GeneMark-ES on assembly
[Oct 15 05:10 PM]: 10,173 predictions from GeneMark
[Oct 15 05:10 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Oct 15 05:14 PM]: 1,021 valid BUSCO predictions found, validating protein sequences
[Oct 15 05:17 PM]: 814 BUSCO predictions validated
[Oct 15 05:17 PM]: Training Augustus using BUSCO gene models
Error: In sequence AgBi.1_256224-258221: One CDS exon does not begin properly after the previous CDS exon.1397 >= 1395
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.1_564660-571196: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.1_933158-940792: One CDS exon does not begin properly after the previous CDS exon.7034 >= 7032
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.1_1283853-1286563: One CDS exon does not begin properly after the previous CDS exon.2110 >= 2108
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_132596-134649: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_178886-183096: One CDS exon does not begin properly after the previous CDS exon.3610 >= 3608
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_428009-429728: One CDS exon does not begin properly after the previous CDS exon.1119 >= 1117
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_559947-568734: One CDS exon does not begin properly after the previous CDS exon.8187 >= 8185
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_732506-737698: One CDS exon does not begin properly after the previous CDS exon.4592 >= 4590
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_815493-820761: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_998134-1000990: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_1109969-1117135: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_1331368-1334325: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.2_1642089-1644291: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_388666-390564: One CDS exon does not begin properly after the previous CDS exon.1298 >= 1296
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_482786-489678: One CDS exon does not begin properly after the previous CDS exon.6292 >= 6290
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_490834-495275: One CDS exon does not begin properly after the previous CDS exon.3841 >= 3839
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_597038-599634: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_641252-643633: One CDS exon does not begin properly after the previous CDS exon.1781 >= 1779
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_792940-794795: One CDS exon does not begin properly after the previous CDS exon.1255 >= 1253
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_893555-895507: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_925232-933158: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1072654-1075143: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1212472-1216841: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1282339-1285614: One CDS exon does not begin properly after the previous CDS exon.577 >= 575
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1410420-1413709: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1469992-1472638: One CDS exon does not begin properly after the previous CDS exon.270 >= 268
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1708488-1710778: One CDS exon does not begin properly after the previous CDS exon.188 >= 186
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_1715194-1717353: One CDS exon does not begin properly after the previous CDS exon.1559 >= 1557
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_2222876-2224041: One CDS exon does not begin properly after the previous CDS exon.1067 >= 1065
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_2269357-2276244: One CDS exon does not begin properly after the previous CDS exon.6287 >= 6285
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.3_2382020-2386135: One CDS exon does not begin properly after the previous CDS exon.3515 >= 3513
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_358039-360513: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_643700-647356: One CDS exon does not begin properly after the previous CDS exon.3056 >= 3054
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_665111-674326: One CDS exon does not begin properly after the previous CDS exon.8615 >= 8613
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_816971-818799: One CDS exon does not begin properly after the previous CDS exon.132 >= 130
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_1255279-1258243: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_1314986-1317486: One CDS exon does not begin properly after the previous CDS exon.1900 >= 1898
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_1702752-1704541: One CDS exon does not begin properly after the previous CDS exon.1189 >= 1187
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_1714189-1718145: One CDS exon does not begin properly after the previous CDS exon.3356 >= 3354
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2304498-2306250: One CDS exon does not begin properly after the previous CDS exon.1152 >= 1150
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2368285-2371164: One CDS exon does not begin properly after the previous CDS exon.2279 >= 2277
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2395052-2397211: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2486390-2494895: One CDS exon does not begin properly after the previous CDS exon.7905 >= 7903
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2515650-2518925: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2523559-2526382: One CDS exon does not begin properly after the previous CDS exon.2223 >= 2221
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_2929544-2933916: One CDS exon does not begin properly after the previous CDS exon.385 >= 383
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.4_3541974-3550243: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.5_538742-541223: One CDS exon does not begin properly after the previous CDS exon.1881 >= 1879
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.5_1229866-1233815: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.5_1338377-1342893: One CDS exon does not begin properly after the previous CDS exon.3916 >= 3914
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.5_1777440-1780211: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.5_1931125-1935690: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.5_2018989-2021512: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_9657-16113: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_425879-429577: One CDS exon does not begin properly after the previous CDS exon.3098 >= 3096
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_493783-497490: One CDS exon does not begin properly after the previous CDS exon.3107 >= 3105
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_518468-524100: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_582385-586487: One CDS exon does not begin properly after the previous CDS exon.3502 >= 3500
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_646064-648200: One CDS exon does not begin properly after the previous CDS exon.1536 >= 1534
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_1167358-1169959: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.6_1583010-1589215: One CDS exon does not begin properly after the previous CDS exon.5605 >= 5603
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_104715-106498: One CDS exon does not begin properly after the previous CDS exon.1183 >= 1181
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_411240-417703: One CDS exon does not begin properly after the previous CDS exon.5863 >= 5861
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_679325-681988: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_1029964-1037029: One CDS exon does not begin properly after the previous CDS exon.7028 >= 7026
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_1247929-1250154: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_1445120-1448283: One CDS exon does not begin properly after the previous CDS exon.2563 >= 2561
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.7_1530987-1536371: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_61878-64836: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_437960-442540: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_624767-632183: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_780477-782880: One CDS exon does not begin properly after the previous CDS exon.1803 >= 1801
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_872858-877836: One CDS exon does not begin properly after the previous CDS exon.4378 >= 4376
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_938378-940746: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_1055355-1056984: One CDS exon does not begin properly after the previous CDS exon.1029 >= 1027
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_1120647-1123481: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_1238434-1242681: One CDS exon does not begin properly after the previous CDS exon.3647 >= 3645
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_1554461-1559602: One CDS exon does not begin properly after the previous CDS exon.4541 >= 4539
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.8_1599727-1600706: One CDS exon does not begin properly after the previous CDS exon.45 >= 43
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.10_133133-135002: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.10_151249-155510: One CDS exon does not begin properly after the previous CDS exon.3661 >= 3659
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.10_450227-456357: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.10_844765-847469: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.14_192519-198746: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.14_350602-353816: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.14_1018658-1020790: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.14_1267688-1272817: One CDS exon does not begin properly after the previous CDS exon.4529 >= 4527
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.15_783185-789479: One CDS exon does not begin properly after the previous CDS exon.5694 >= 5692
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.16_92637-96586: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.16_259936-262363: One CDS exon does not begin properly after the previous CDS exon.20 >= 18
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.16_594567-596396: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.16_654735-659834: One CDS exon does not begin properly after the previous CDS exon.4499 >= 4497
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_1399125-1402391: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_1835529-1837274: One CDS exon does not begin properly after the previous CDS exon.1145 >= 1143
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_1945888-1947523: One CDS exon does not begin properly after the previous CDS exon.1035 >= 1033
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_1971922-1974329: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_2088447-2093915: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_2148546-2153729: One CDS exon does not begin properly after the previous CDS exon.4583 >= 4581
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence AgBi.18_2932807-2937109: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.

augustus: ERROR
No genbank sequences found.

Traceback (most recent call last):
File "/public/home/liuyuanchao/software/anaconda3/envs/funannotate/bin/funannotate", line 10, in
sys.exit(main())
File "/public/home/liuyuanchao/software/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 717, in main
mod.main(arguments)
File "/public/home/liuyuanchao/software/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 2094, in main
lib.trainAugustus(
File "/public/home/liuyuanchao/software/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py", line 10971, in trainAugustus
train_results = getTrainResults(
File "/public/home/liuyuanchao/software/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py", line 10708, in getTrainResults
float(values1[1]),
UnboundLocalError: local variable 'values1' referenced before assignment

OS/Install Information
$funannotate check --show-versions

Checking dependencies for 1.8.17

You are running Python v 3.8.19. Now checking python packages...
biopython: 1.79
goatools: 1.4.12
matplotlib: 3.7.3
natsort: 8.4.0
numpy: 1.24.4
pandas: 2.0.3
psutil: 6.0.0
requests: 2.32.3
scikit-learn: 1.3.2
scipy: 1.10.1
seaborn: 0.13.2
All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules...
Carp: 1.50
Clone: 0.46
DBD::SQLite: 1.72
DBD::mysql: 4.050
DBI: 1.643
DB_File: 1.858
Data::Dumper: 2.183
File::Basename: 2.85
File::Which: 1.24
Getopt::Long: 2.58
Hash::Merge: 0.302
JSON: 4.10
LWP::UserAgent: 6.67
Logger::Simple: 2.0
POSIX: 1.94
Parallel::ForkManager: 2.03
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.14
Tie::File: 1.06
URI::Escape: 5.17
YAML: 1.30
local::lib: 2.000029
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/public/home/user/software/funannotate/database
$PASAHOME=/public/home/user/software/anaconda3/envs/funannotate/opt/pasa-2.5.3
$TRINITY_HOME=/public/home/user/software/anaconda3/envs/funannotate/opt/trinity-2.15.2
$EVM_HOME=/public/home/user/software/anaconda3/envs/funannotate/opt/evidencemodeler-2.1.0
$AUGUSTUS_CONFIG_PATH=/public/home/user/software/anaconda3/envs/funannotate/config/
$GENEMARK_PATH=/public/home/user/software/GeneMark/gmes_linux_64_4
All 6 environmental variables are set

Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.15.2
augustus: 3.5.0
bamtools: bamtools 2.5.2
bedtools: bedtools v2.31.1
blat: BLAT v39x1
diamond: 2.1.8
emapper.py: 2.1.12
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2021-08-25
gmes_petap.pl: 4.68_lic
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 22.0.1-internal
kallisto: 0.46.1
mafft: v7.526 (2024/Apr/26)
makeblastdb: makeblastdb 2.16.0+
minimap2: 2.28-r1209
pigz: 2.8
proteinortho: 6.3.2
pslCDnaFilter: no way to determine
salmon: salmon 1.10.3
samtools: samtools 1.9
signalp: 5.0b
snap: 2006-07-28
stringtie: 2.2.3
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 50
tbl2asn: 25.8
tblastn: tblastn 2.16.0+
trimal: trimAl v1.5.rev0 build[2024-05-27]
trimmomatic: 0.39
All 37 external dependencies are installed

[hyphaltip]

this is weird that snap / fathom should have fixed orientation of exons for the training that comes from BUSCO. I've not seen this but @nextgenusfs we can maybe take a look at what is happening in the prediction.

[CallinCeriani]

Hello @hyphaltip and @nextgenusfs, I am having the same problem.

[jpaulsen0623]

@hyphaltip and @nextgenusfs I am also having these errors with my own data! Any solutions or insights yet?

[nextgenusfs]

Apologies I've not had a chance yet to dig in. But on the surface it looks like BUSCO perhaps failed.

Can someone share a genome and the corresponding out/predict_misc/busco.final.gff3 -- that's the input file for training which appears to be the problem.

My guess is that it's an Augustus compilation problem resulting in incomplete results from BUSCO. Its nearly always Augustus.....

[jpaulsen0623]

Heres a dropbox link with a genome and the corresponding busco.final.gff3

https://www.dropbox.com/scl/fo/m9x33hnn3imhjtsh8n9js/AGSJ6H-lTQmKoaM0LEktZWQ?rlkey=ec68lqjljizsmbg5koavpoeow&st=kx7gfx5l&dl=0

[nextgenusfs]

Thanks @jpaulsen0623, doesn't appear to be anything obviously wrong with this file. From this error report seems like error is emanating from Augustus.. https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?t=33

Is Augustus installed from conda? Anyway to install Augustus differently, I still think its quite possible it's a compilation error in Augustus (might be in a specific conda build, ie you could try a different build for v3.5.0. Looks like there are 5 of them....

augustus                       3.5.0 pl5321h1fe13c5_0  bioconda            
augustus                       3.5.0 pl5321h1fe13c5_1  bioconda            
augustus                       3.5.0 pl5321h3798a5e_3  bioconda            
augustus                       3.5.0 pl5321h7a4bd8d_2  bioconda            
augustus                       3.5.0 pl5321h8ad343c_4  bioconda  

Something like this to get full version and build info from your current env: conda list -e | grep 'augustus'

[liuyca1]

Dear Palme Thanks for your reply. I checked the version of Augustus and it is already 3.5.0 (build number is pl5321h95201ac_4 from bioconda), but it still reports an error.

…

------------------ 原始邮件 ------------------ 发件人: "nextgenusfs/funannotate" ***@***.***>; 发送时间: 2024年10月23日(星期三) 上午7:27 ***@***.***>; ***@***.******@***.***>; 主题: Re: [nextgenusfs/funannotate] funannotate predict errors (Issue #1072) Thanks @jpaulsen0623, doesn't appear to be anything obviously wrong with this file. From this error report seems like error is emanating from Augustus.. https://bioinf.uni-greifswald.de/bioinf/forum/viewtopic.php?t=33 Is Augustus installed from conda? Anyway to install Augustus differently, I still think its quite possible it's a compilation error in Augustus (might be in a specific conda build, ie you could try a different build for v3.5.0. Looks like there are 5 of them.... augustus 3.5.0 pl5321h1fe13c5_0 bioconda augustus 3.5.0 pl5321h1fe13c5_1 bioconda augustus 3.5.0 pl5321h3798a5e_3 bioconda augustus 3.5.0 pl5321h7a4bd8d_2 bioconda augustus 3.5.0 pl5321h8ad343c_4 bioconda — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[nextgenusfs]

Yeah, that build seems to be the problem. Need to install a different build or install Augustus a different way. Funannotate only cares that it's in the PATH, it doesn't need to be a conda build. There are many ways to link it to the conda environment.

[liuyca1]

Yeah, that build seems to be the problem. Need to install a different build or install Augustus a different way. Funannotate only cares that it's in the PATH, it doesn't need to be a conda build. There are many ways to link it to the conda environment.

Augustus installation depends on a specific version of boost-cpp (1.85.0), so you need to install the Augustus software that matches the boost-cpp version.
First run the following command
$mamba search augustus=3.5.0 --info
Loading channels: done
augustus 3.5.0 pl5321h700735d_3

file name : augustus-3.5.0-pl5321h700735d_3.tar.bz2
name : augustus
version : 3.5.0
build : pl5321h700735d_3
build number: 3
size : 31.3 MB
license : Artistic Licence
subdir : linux-64
url : https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321h700735d_3.tar.bz2
md5 : 154da88311347665ab2368303391d6e8
timestamp : 2023-05-16 15:51:09 UTC
dependencies:

• bamtools >=2.5.1,<2.5.2.0a0
• biopython
  - boost-cpp >=1.78.0,<1.78.1.0a0
• cdbtools
• diamond
• gsl >=2.7,<2.8.0a0
• htslib >=1.17,<1.22.0a0
• libblas >=3.9.0,<4.0a0
• libcblas >=3.9.0,<4.0a0
• libgcc-ng >=12
• libsqlite >=3.41.2,<4.0a0
• libstdcxx-ng >=12
• libzlib >=1.2.13,<1.3.0a0
• lp_solve
• perl >=5.32.1,<5.33.0a0 *_perl5
• perl-app-cpanminus
• perl-dbi
• perl-file-which
• perl-module-build 0.4234.*
• perl-parallel-forkmanager
• perl-scalar-list-utils
• perl-yaml
• sqlite
• suitesparse >=5.10.1,<6.0a0
• tar
• ucsc-fatotwobit
• ucsc-twobitinfo
• zlib

augustus 3.5.0 pl5321h816be78_2

file name : augustus-3.5.0-pl5321h816be78_2.tar.bz2
name : augustus
version : 3.5.0
build : pl5321h816be78_2
build number: 2
size : 31.2 MB
license : Artistic Licence
subdir : linux-64
url : https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321h816be78_2.tar.bz2
md5 : f71b2b09b9884742f0bb5e86a652e80d
timestamp : 2023-03-07 04:47:40 UTC
dependencies:

• bamtools >=2.5.1,<2.5.2.0a0
• biopython
  - boost-cpp >=1.74.0,<1.74.1.0a0
• cdbtools
• diamond
• gsl >=2.7,<2.8.0a0
• htslib >=1.17,<1.22.0a0
• libblas >=3.9.0,<4.0a0
• libcblas >=3.9.0,<4.0a0
• libgcc-ng >=12
• libsqlite >=3.40.0,<4.0a0
• libstdcxx-ng >=12
• libzlib >=1.2.13,<1.3.0a0
• lp_solve
• perl >=5.32.1,<5.33.0a0 *_perl5
• perl-app-cpanminus
• perl-dbi
• perl-file-which
• perl-module-build 0.4232.*
• perl-parallel-forkmanager
• perl-scalar-list-utils
• perl-yaml
• sqlite >=3.40.0,<4.0a0
• suitesparse >=5.10.1,<6.0a0
• tar
• ucsc-fatotwobit
• ucsc-twobitinfo
• zlib >=1.2.13,<1.3.0a0

augustus 3.5.0 pl5321h95201ac_4

file name : augustus-3.5.0-pl5321h95201ac_4.tar.bz2
name : augustus
version : 3.5.0
build : pl5321h95201ac_4
build number: 4
size : 31.2 MB
license : Artistic Licence
subdir : linux-64
url : https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321h95201ac_4.tar.bz2
md5 : 6cba5e1db7be3f7eb137d7dc7f88ff04
timestamp : 2024-06-06 22:13:32 UTC
dependencies:

• bamtools >=2.5.2,<2.6.0a0
• biopython
  - boost-cpp
• cdbtools
• diamond
• gsl >=2.7,<2.8.0a0
• htslib >=1.17,<1.22.0a0
• libblas >=3.9.0,<4.0a0
• libcblas >=3.9.0,<4.0a0
• libgcc-ng >=12
• libsqlite >=3.45.3,<4.0a0
• libstdcxx-ng >=12
• libzlib >=1.2.13,<2.0a0
• lp_solve
• perl >=5.32.1,<5.33.0a0 *_perl5
• perl-app-cpanminus
• perl-dbi
• perl-file-which
• perl-module-build 0.4234.*
• perl-parallel-forkmanager
• perl-scalar-list-utils
• perl-yaml
• sqlite
• suitesparse >=5.10.1,<6.0a0
• tar
• ucsc-fatotwobit
• ucsc-twobitinfo
• zlib

augustus 3.5.0 pl5321hf46c7bb_0

file name : augustus-3.5.0-pl5321hf46c7bb_0.tar.bz2
name : augustus
version : 3.5.0
build : pl5321hf46c7bb_0
build number: 0
size : 31.2 MB
license : Artistic Licence
subdir : linux-64
url : https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321hf46c7bb_0.tar.bz2
md5 : 795c56fff4314188461da94e3edd27b7
timestamp : 2022-10-09 02:13:23 UTC
dependencies:

• bamtools >=2.5.1,<2.5.2.0a0
• biopython
• boost-cpp >=1.74.0,<1.74.1.0a0
• cdbtools
• diamond
• gsl >=2.7,<2.8.0a0
• htslib >=1.16,<1.22.0a0
• libblas >=3.9.0,<4.0a0
• libcblas >=3.9.0,<4.0a0
• libgcc-ng >=12
• libsqlite >=3.39.4,<4.0a0
• libstdcxx-ng >=12
• libzlib >=1.2.12,<1.3.0a0
• lp_solve
• perl >=5.32.1,<5.33.0a0 *_perl5
• perl-app-cpanminus
• perl-dbi
• perl-file-which
• perl-module-build
• perl-parallel-forkmanager
• perl-scalar-list-utils
• perl-yaml
• sqlite >=3.39.4,<4.0a0
• suitesparse >=5.10.1,<6.0a0
• tar
• ucsc-fatotwobit
• ucsc-twobitinfo
• zlib >=1.2.12,<1.3.0a0

augustus 3.5.0 pl5321hf46c7bb_1

file name : augustus-3.5.0-pl5321hf46c7bb_1.tar.bz2
name : augustus
version : 3.5.0
build : pl5321hf46c7bb_1
build number: 1
size : 31.2 MB
license : Artistic Licence
subdir : linux-64
url : https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321hf46c7bb_1.tar.bz2
md5 : dd79853c40921190781b199a7550f64b
timestamp : 2022-10-18 10:22:09 UTC
dependencies:

• bamtools >=2.5.1,<2.5.2.0a0
• biopython
• boost-cpp >=1.74.0,<1.74.1.0a0
• cdbtools
• diamond
• gsl >=2.7,<2.8.0a0
• htslib >=1.16,<1.22.0a0
• libblas >=3.9.0,<4.0a0
• libcblas >=3.9.0,<4.0a0
• libgcc-ng >=12
• libsqlite >=3.39.4,<4.0a0
• libstdcxx-ng >=12
• libzlib >=1.2.13,<1.3.0a0
• lp_solve
• perl >=5.32.1,<5.33.0a0 *_perl5
• perl-app-cpanminus
• perl-dbi
• perl-file-which
• perl-module-build
• perl-parallel-forkmanager
• perl-scalar-list-utils
• perl-yaml
• sqlite >=3.39.4,<4.0a0
• suitesparse >=5.10.1,<6.0a0
• tar
• ucsc-fatotwobit
• ucsc-twobitinfo
• zlib >=1.2.13,<1.3.0a0

$mamba install augustus=3.5.0=pl5321h95201ac_4
Looking for: ['augustus==3.5.0=pl5321h95201ac_4']

conda-forge/noarch Using cache
bioconda/linux-64 Using cache
bioconda/noarch Using cache
pkgs/main/linux-64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/linux-64 No change
conda-forge/linux-64 46.0MB @ 1.2MB/s 39.7s

Pinned packages:

• python 3.8.*

Transaction

Prefix: /public/home/liuyuanchao/software/anaconda3/envs/funannotate

All requested packages already installed

$mamba list augustus

packages in environment at /public/home/liuyuanchao/software/anaconda3/envs/funannotate:

Name Version Build Channel

augustus 3.5.0 pl5321h95201ac_4 bioconda

The above are the installation steps and results, and then test the software
$funannotate check --show-versions

Checking dependencies for 1.8.17

You are running Python v 3.8.19. Now checking python packages...
biopython: 1.79
goatools: 1.2.3
matplotlib: 3.7.3
natsort: 8.4.0
numpy: 1.24.4
pandas: 2.0.3
psutil: 6.0.0
requests: 2.32.3
scikit-learn: 1.3.2
scipy: 1.10.1
seaborn: 0.13.2
All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules...
Carp: 1.38
Clone: 0.46
DBD::SQLite: 1.72
DBD::mysql: 4.046
DBI: 1.643
DB_File: 1.858
Data::Dumper: 2.183
File::Basename: 2.85
File::Which: 1.24
Getopt::Long: 2.58
Hash::Merge: 0.302
JSON: 4.10
LWP::UserAgent: 6.67
Logger::Simple: 2.0
POSIX: 1.94
Parallel::ForkManager: 2.03
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.14
Tie::File: 1.06
URI::Escape: 5.12
YAML: 1.30
local::lib: 2.000029
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/public/home/user/software/funannotate/database/funannotate_basic
$PASAHOME=/public/home/user/software/anaconda3/envs/funannotate/opt/pasa-2.5.3
$TRINITY_HOME=/public/home/user/software/anaconda3/envs/funannotate/opt/trinity-2.15.2
$EVM_HOME=/public/home/user/software/anaconda3/envs/funannotate/opt/evidencemodeler-2.1.0
$AUGUSTUS_CONFIG_PATH=/public/home/user/software/anaconda3/envs/funannotate/config/
$GENEMARK_PATH=/public/home/user/software/GeneMark/gmes_linux_64_4/gmes_petap.pl
All 6 environmental variables are set

Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.15.2
augustus: 3.5.0
bamtools: bamtools 2.5.2
bedtools: bedtools v2.31.1
blat: BLAT v39x1
diamond: 2.1.10
emapper.py: 2.1.12
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2023-12-01
gmes_petap.pl: 4.71_lic
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 22.0.1-internal
kallisto: 0.46.1
mafft: v7.525 (2024/Mar/13)
makeblastdb: makeblastdb 2.16.0+
minimap2: 2.28-r1209
pigz: 2.8
proteinortho: 6.3.2
pslCDnaFilter: no way to determine
salmon: salmon 1.10.3
samtools: samtools 1.9
signalp: 6.0
snap: 2006-07-28
stringtie: 2.2.3
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 50
tbl2asn: 25.8
tblastn: tblastn 2.16.0+
trimal: trimAl v1.5.rev0 build[2024-05-27]
trimmomatic: 0.39
All 37 external dependencies are installed

I ran funannotate predict again, but the same error occurred.

$funannotate predict -i Genomic_masked3.fna --species "Scytalidium ganodermophthorum" -o ./fun --busco_seed_species anidulans --busco_db dikarya --min_training_models 150 --cpus 80

[Oct 24 04:23 PM]: OS: CentOS Linux 7, 80 cores, ~ 1584 GB RAM. Python: 3.8.19
[Oct 24 04:23 PM]: Running funannotate v1.8.17
[Oct 24 04:23 PM]: Skipping CodingQuarry as no --rna_bam passed
[Oct 24 04:23 PM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus busco
genemark selftraining
glimmerhmm busco
snap busco
[Oct 24 04:23 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Oct 24 04:23 PM]: Genome loaded: 140 scaffolds; 42,127,880 bp; 4.20% repeats masked
/public/home/user/software/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-p2g.py:14: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import parse_version
[Oct 24 04:24 PM]: Mapping 559,318 proteins to genome using diamond and exonerate
[Oct 24 04:27 PM]: Found 312,027 preliminary alignments with diamond in 0:01:35 --> generated FASTA files for exonerate in 0:01:55
Progress: 312027 complete, 0 failed, 0 remaining
[Oct 24 04:38 PM]: Exonerate finished in 0:10:08: found 1,610 alignments
[Oct 24 04:38 PM]: Running GeneMark-ES on assembly
[Oct 24 04:50 PM]: 13,741 predictions from GeneMark
[Oct 24 04:50 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Oct 24 04:55 PM]: 1,265 valid BUSCO predictions found, validating protein sequences
[Oct 24 04:57 PM]: 811 BUSCO predictions validated
[Oct 24 04:57 PM]: Training Augustus using BUSCO gene models
Error: In sequence scaffold_1_288249-291853: One CDS exon does not begin properly after the previous CDS exon.3004 >= 3002
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_429234-432515: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_747250-749787: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_1543618-1548173: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_1599986-1602078: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_1654479-1658631: One CDS exon does not begin properly after the previous CDS exon.3552 >= 3550
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_1759345-1761516: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_1852963-1858021: One CDS exon does not begin properly after the previous CDS exon.4458 >= 4456
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_1967538-1972397: One CDS exon does not begin properly after the previous CDS exon.4259 >= 4257
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_2273800-2275903: One CDS exon does not begin properly after the previous CDS exon.1503 >= 1501
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_2481945-2487910: One CDS exon does not begin properly after the previous CDS exon.5365 >= 5363
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_2600378-2604432: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_2808437-2813161: One CDS exon does not begin properly after the previous CDS exon.4124 >= 4122
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_1_3130617-3132699: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1456136-1459274: One CDS exon does not begin properly after the previous CDS exon.2538 >= 2536
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1507912-1511109: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1512716-1516425: One CDS exon does not begin properly after the previous CDS exon.3109 >= 3107
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1530451-1532918: One CDS exon does not begin properly after the previous CDS exon.2044 >= 2042
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1543457-1546163: One CDS exon does not begin properly after the previous CDS exon.2106 >= 2104
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1715552-1717628: One CDS exon does not begin properly after the previous CDS exon.1476 >= 1474
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1804368-1809772: One CDS exon does not begin properly after the previous CDS exon.4804 >= 4802
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1836063-1838858: One CDS exon does not begin properly after the previous CDS exon.2195 >= 2193
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_1984955-1987654: One CDS exon does not begin properly after the previous CDS exon.2099 >= 2097
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_2_2275870-2277384: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_21578-27572: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_166104-167963: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_245946-249885: One CDS exon does not begin properly after the previous CDS exon.3339 >= 3337
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_982588-985632: One CDS exon does not begin properly after the previous CDS exon.2444 >= 2442
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_1046663-1051586: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_1543142-1545975: One CDS exon does not begin properly after the previous CDS exon.2233 >= 2231
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_1598097-1600927: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_3_1788621-1792015: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_123533-125731: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_345039-347420: One CDS exon does not begin properly after the previous CDS exon.1781 >= 1779
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_375442-377475: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_547160-551346: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_1323596-1329936: One CDS exon does not begin properly after the previous CDS exon.5740 >= 5738
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_4_1485376-1487523: One CDS exon does not begin properly after the previous CDS exon.1547 >= 1545
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_268889-270753: One CDS exon does not begin properly after the previous CDS exon.1590 >= 1588
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_5_328514-331470: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_908067-910010: One CDS exon does not begin properly after the previous CDS exon.1343 >= 1341
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_1033858-1038377: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_1061125-1065112: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_6_1187381-1190727: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_88551-92695: One CDS exon does not begin properly after the previous CDS exon.3544 >= 3542
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_106226-107489: One CDS exon does not begin properly after the previous CDS exon.94 >= 92
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_699793-703287: One CDS exon does not begin properly after the previous CDS exon.3066 >= 3064
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_774863-777130: One CDS exon does not begin properly after the previous CDS exon.1667 >= 1665
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_7_942776-945481: One CDS exon does not begin properly after the previous CDS exon.2105 >= 2103
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_8_172120-175352: One CDS exon does not begin properly after the previous CDS exon.321 >= 319
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_8_302296-305654: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_8_610956-613774: One CDS exon does not begin properly after the previous CDS exon.2218 >= 2216
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_8_644502-646835: One CDS exon does not begin properly after the previous CDS exon.1733 >= 1731
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_8_687595-692089: One CDS exon does not begin properly after the previous CDS exon.3894 >= 3892
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_8_856399-858551: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_49071-52234: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_171622-173106: One CDS exon does not begin properly after the previous CDS exon.261 >= 259
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_237300-240539: One CDS exon does not begin properly after the previous CDS exon.2639 >= 2637
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_316826-321228: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_385846-387651: One CDS exon does not begin properly after the previous CDS exon.1205 >= 1203
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 0 annotations.
Error: In sequence scaffold_9_798126-800049: One CDS exon does not begin properly after the previous CDS exon.1323 >= 1321
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_9_863071-865390: One CDS exon does not begin properly after the previous CDS exon.1719 >= 1717
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_9_916772-920541: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_9_1147770-1150369: One CDS exon does not begin properly after the previous CDS exon.1999 >= 1997
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_10_348491-351039: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_10_641381-643945: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_10_713818-718747: One CDS exon does not begin properly after the previous CDS exon.4329 >= 4327
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_10_845638-847513: One CDS exon does not begin properly after the previous CDS exon.1275 >= 1273
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_11_564375-565984: One CDS exon does not begin properly after the previous CDS exon.1459 >= 1457
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_11_989731-994019: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_13_754789-756617: One CDS exon does not begin properly after the previous CDS exon.1658 >= 1656
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_14_244562-246894: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_14_386375-387957: One CDS exon does not begin properly after the previous CDS exon.982 >= 980
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_14_563179-565116: One CDS exon does not begin properly after the previous CDS exon.80 >= 78
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_14_897242-899925: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_15_170059-172352: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_15_329611-331710: One CDS exon does not begin properly after the previous CDS exon.1499 >= 1497
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_15_625294-626685: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_15_829232-832852: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_16_139735-141257: One CDS exon does not begin properly after the previous CDS exon.922 >= 920
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_16_168921-170677: One CDS exon does not begin properly after the previous CDS exon.1156 >= 1154
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_16_495870-498548: One CDS exon does not begin properly after the previous CDS exon.2078 >= 2076
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_16_745540-752944: One CDS exon does not begin properly after the previous CDS exon.6804 >= 6802
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_17_534179-537789: One CDS exon does not begin properly after the previous CDS exon.3010 >= 3008
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_17_640273-643395: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_17_929580-932717: One CDS exon does not begin properly after the previous CDS exon.2537 >= 2535
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_18_445212-447969: One CDS exon does not begin properly after the previous CDS exon.2157 >= 2155
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_18_671622-674243: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_21_253170-254278: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_21_344437-346352: One CDS exon does not begin properly after the previous CDS exon.1315 >= 1313
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_23_183695-186827: One CDS exon does not begin properly after the previous CDS exon.2532 >= 2530
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_23_210453-212845: One CDS exon does not begin properly after the previous CDS exon.1792 >= 1790
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_32_120733-124724: One CDS exon does not begin properly after the previous CDS exon.3391 >= 3389
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_33_59089-63159: One CDS exon does not begin properly after the previous CDS exon.3470 >= 3468
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_33_90848-93702: One CDS exon does not begin properly after the previous CDS exon.542 >= 540
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_33_141621-145515: One CDS exon does not begin properly after the previous CDS exon.3294 >= 3292
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_33_286129-288801: One CDS exon does not begin properly after the previous CDS exon.2072 >= 2070
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_33_321274-327291: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
Error: In sequence scaffold_47_123861-126250: One CDS exon does not begin properly after the previous CDS exon.1789 >= 1787
GBProcessor::getGeneList(): Intron has non-positive length.
Encountered error after reading 1 annotations.
[Oct 24 04:57 PM]: Augustus initial training results:
Feature Specificity Sensitivity
nucleotides 100.0% 100.0%
exons 100.0% 100.0%
genes 100.0% 100.0%
[Oct 24 04:57 PM]: Running Augustus gene prediction using scytalidium_ganodermophthorum parameters
Progress: 195 complete, 0 failed, 0 remaining
[Oct 24 04:58 PM]: 8,157 predictions from Augustus
[Oct 24 04:58 PM]: Pulling out high quality Augustus predictions
[Oct 24 04:58 PM]: Found 35 high quality predictions from Augustus (>90% exon evidence)
[Oct 24 04:58 PM]: Running SNAP gene prediction, using training data: ./fun/predict_misc/busco.final.gff3
[Oct 24 05:00 PM]: 0 predictions from SNAP
[Oct 24 05:00 PM]: SNAP prediction failed, moving on without result
[Oct 24 05:00 PM]: Running GlimmerHMM gene prediction, using training data: ./fun/predict_misc/busco.final.gff3
[Oct 24 05:16 PM]: 11,427 predictions from GlimmerHMM
[Oct 24 05:16 PM]: Summary of gene models passed to EVM (weights):
Source Weight Count
Augustus 1 8122
Augustus HiQ 2 35
GeneMark 1 13741
GlimmerHMM 1 11427
Total - 33325
[Oct 24 05:16 PM]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval
Progress: 406 complete, 0 failed, 0 remaining
[Oct 24 05:18 PM]: Converting to GFF3 and collecting all EVM results
[Oct 24 05:18 PM]: 12,413 total gene models from EVM
[Oct 24 05:18 PM]: Generating protein fasta files from 12,413 EVM models
[Oct 24 05:18 PM]: now filtering out bad gene models (< 50 aa in length, transposable elements, etc).
[Oct 24 05:18 PM]: Found 27 gene models to remove: 3 too short; 1 span gaps; 23 transposable elements
[Oct 24 05:18 PM]: 12,386 gene models remaining
[Oct 24 05:18 PM]: Predicting tRNAs
[Oct 24 05:22 PM]: 118 tRNAscan models are valid (non-overlapping)
[Oct 24 05:22 PM]: Generating GenBank tbl annotation file
[Oct 24 05:23 PM]: Collecting final annotation files for 12,504 total gene models
[Oct 24 05:23 PM]: Converting to final Genbank format
[Oct 24 05:24 PM]: Funannotate predict is finished, output files are in the ./fun/predict_results folder
[Oct 24 05:24 PM]: Your next step might be functional annotation, suggested commands:

Run InterProScan (manual install):
funannotate iprscan -i ./fun -c 80

Run antiSMASH (optional):
funannotate remote -i ./fun -m antismash -e [email protected]

Annotate Genome:
funannotate annotate -i ./fun --cpus 80 --sbt yourSBTfile.txt

[Oct 24 05:24 PM]: Training parameters file saved: ./fun/predict_results/scytalidium_ganodermophthorum.parameters.json
[Oct 24 05:24 PM]: Add species parameters to database:

funannotate species -s scytalidium_ganodermophthorum -a ./fun/predict_results/scytalidium_ganodermophthorum.parameters.json

[liuyca1]

Yeah, that build seems to be the problem. Need to install a different build or install Augustus a different way. Funannotate only cares that it's in the PATH, it doesn't need to be a conda build. There are many ways to link it to the conda environment.

But when I removed some parameters (--busco_seed_species anidulans --busco_db dikarya --min_training_models 150) and re-ran it, no error was reported

$funannotate predict -i Genomic_masked3.fna --species "Scytalidium ganodermophthorum" -o ./fun --cpus 80

[Oct 24 06:30 PM]: OS: CentOS Linux 7, 80 cores, ~ 1584 GB RAM. Python: 3.8.19
[Oct 24 06:30 PM]: Running funannotate v1.8.17
[Oct 24 06:30 PM]: Skipping CodingQuarry as no --rna_bam passed
[Oct 24 06:30 PM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus busco
genemark selftraining
glimmerhmm busco
snap busco
[Oct 24 06:30 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Oct 24 06:30 PM]: Genome loaded: 140 scaffolds; 42,127,880 bp; 4.20% repeats masked
[Oct 24 06:30 PM]: Existing protein alignments found: ./fun/predict_misc/protein_alignments.gff3
[Oct 24 06:30 PM]: Existing GeneMark annotation found: ./fun/predict_misc/genemark.gff
[Oct 24 06:30 PM]: 13,741 predictions from GeneMark
[Oct 24 06:30 PM]: Existing BUSCO results found: ./fun/predict_misc/busco.final.gff3 containing 811 predictions
[Oct 24 06:30 PM]: Existing Augustus annotations found: ./fun/predict_misc/augustus.gff3
[Oct 24 06:30 PM]: Pulling out high quality Augustus predictions
[Oct 24 06:30 PM]: Found 35 high quality predictions from Augustus (>90% exon evidence)
[Oct 24 06:30 PM]: Existing snap predictions found ./fun/predict_misc/snap-predictions.gff3
[Oct 24 06:30 PM]: 0 predictions from SNAP
[Oct 24 06:30 PM]: SNAP prediction failed, moving on without result
[Oct 24 06:30 PM]: Existing GlimmerHMM predictions found: ./fun/predict_misc/glimmerhmm-predictions.gff3
[Oct 24 06:30 PM]: 11,427 predictions from GlimmerHMM
[Oct 24 06:30 PM]: Summary of gene models passed to EVM (weights):
Source Weight Count
Augustus 1 8122
Augustus HiQ 2 35
GeneMark 1 13741
GlimmerHMM 1 11427
Total - 33325
[Oct 24 06:30 PM]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval
Progress: 406 complete, 0 failed, 0 remaining
[Oct 24 06:32 PM]: Converting to GFF3 and collecting all EVM results
[Oct 24 06:32 PM]: 12,414 total gene models from EVM
[Oct 24 06:32 PM]: Generating protein fasta files from 12,414 EVM models
[Oct 24 06:32 PM]: now filtering out bad gene models (< 50 aa in length, transposable elements, etc).
[Oct 24 06:32 PM]: Found 27 gene models to remove: 3 too short; 1 span gaps; 23 transposable elements
[Oct 24 06:32 PM]: 12,387 gene models remaining
[Oct 24 06:32 PM]: Predicting tRNAs
[Oct 24 06:32 PM]: 118 tRNAscan models are valid (non-overlapping)
[Oct 24 06:32 PM]: Generating GenBank tbl annotation file
[Oct 24 06:33 PM]: Collecting final annotation files for 12,505 total gene models
[Oct 24 06:33 PM]: Converting to final Genbank format
[Oct 24 06:34 PM]: Funannotate predict is finished, output files are in the ./fun/predict_results folder
[Oct 24 06:34 PM]: Your next step might be functional annotation, suggested commands:

Run InterProScan (manual install):
funannotate iprscan -i ./fun -c 80

Run antiSMASH (optional):
funannotate remote -i ./fun -m antismash -e [email protected]

Annotate Genome:
funannotate annotate -i ./fun --cpus 80 --sbt yourSBTfile.txt

[Oct 24 06:34 PM]: Training parameters file saved: ./fun/predict_results/scytalidium_ganodermophthorum.parameters.json
[Oct 24 06:34 PM]: Add species parameters to database:

funannotate species -s scytalidium_ganodermophthorum -a ./fun/predict_results/scytalidium_ganodermophthorum.parameters.json

[mencian]

I've rebuilt augustus here, could you see if the new Augustus build fixes the issue?

[liuyca1]

Thank you very much, but due to the lack of necessary programming skills and the problem of server root permissions, I still cannot complete the repair. Can you provide an updated Augustus installation package? Then, I will try to replace the existing version. I am very much looking forward to it.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "nextgenusfs/funannotate" ***@***.***&gt;; 发送时间:&nbsp;2024年10月25日(星期五) 上午7:16 ***@***.***&gt;; ***@***.******@***.***&gt;; 主题:&nbsp;Re: [nextgenusfs/funannotate] funannotate predict errors (Issue #1072) I've rebuilt augustus here, could you see if the new Augustus build fixes the issue? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;