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funannotate predict errors #1072

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liuyca1 opened this issue Oct 15, 2024 · 8 comments
Open

funannotate predict errors #1072

liuyca1 opened this issue Oct 15, 2024 · 8 comments

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@liuyca1
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liuyca1 commented Oct 15, 2024

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

@jpaulsen0623
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@hyphaltip and @nextgenusfs I am also having these errors with my own data! Any solutions or insights yet?

@nextgenusfs
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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
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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
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nextgenusfs commented Oct 22, 2024 •
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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
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liuyca1 commented Oct 23, 2024 via email

@nextgenusfs
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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.

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@hyphaltip @nextgenusfs @liuyca1 @jpaulsen0623 @CallinCeriani