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Published 20 hours ago • verified publisher icon nextgenusfs

funannotate predict errors

Open liuyca1 opened this issue 1 year ago • 2 comments

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

liuyca1 avatar Oct 15 '24 11:10 liuyca1

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.

hyphaltip avatar Oct 15 '24 16:10 hyphaltip

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

CallinCeriani avatar Oct 18 '24 05:10 CallinCeriani

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

jpaulsen0623 avatar Oct 22 '24 21:10 jpaulsen0623

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.....

nextgenusfs avatar Oct 22 '24 21:10 nextgenusfs

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

jpaulsen0623 avatar Oct 22 '24 22:10 jpaulsen0623

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'

nextgenusfs avatar Oct 22 '24 23:10 nextgenusfs

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: @.***>

liuyca1 avatar Oct 23 '24 00:10 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.

nextgenusfs avatar Oct 23 '24 14:10 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.

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 avatar Oct 24 '24 10:10 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

liuyca1 avatar Oct 24 '24 10:10 liuyca1

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

mencian avatar Oct 24 '24 23:10 mencian

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.

------------------ 原始邮件 ------------------ 发件人: "nextgenusfs/funannotate" @.>; 发送时间: 2024年10月25日(星期五) 上午7:16 @.>; @.@.>; 主题: 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: @.***>

liuyca1 avatar Oct 29 '24 02:10 liuyca1 

(funannotate) [root@localhost funannotate]# funannotate predict -i ../data/genomes.fasta -o fun -s "th" --rna_bam ../data/rnaalign.bam --protein_evidence ../data/all.pep.fasta --transcript_evidence ../data/Trinity.fasta --cpus 8
-------------------------------------------------------
[Jan 06 09:38 PM]: OS: CentOS Linux 7, 8 cores, ~ 16 GB RAM. Python: 3.9.19
[Jan 06 09:38 PM]: Running funannotate v1.8.17
[Jan 06 09:38 PM]: Parsed training data, run ab-initio gene predictors as follows:
  Program        Training-Method
  augustus       busco          
  codingquarry   rna-bam        
  genemark       selftraining   
  glimmerhmm     busco          
  snap           busco          
[Jan 06 09:39 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Jan 06 09:39 PM]: Genome loaded: 21 scaffolds; 42,535,831 bp; 9.52% repeats masked
[Jan 06 09:39 PM]: Aligning transcript evidence to genome with minimap2
[Jan 06 09:39 PM]: Found 36,142 alignments, wrote GFF3 and Augustus hints to file
[Jan 06 09:39 PM]: Extracting hints from RNA-seq BAM file using bam2hints
/root/miniconda3/envs/funannotate/lib/python3.9/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
[Jan 06 09:44 PM]: Mapping 72,501 proteins to genome using diamond and exonerate
[Jan 06 09:46 PM]: Found 71,223 preliminary alignments with diamond in 0:01:21 --> generated FASTA files for exonerate in 0:00:12
     Progress: 71223 complete, 0 failed, 0 remaining            
[Jan 06 10:01 PM]: Exonerate finished in 0:15:03: found 2,195 alignments
[Jan 06 10:01 PM]: Running GeneMark-ES on assembly
[Jan 06 10:22 PM]: 14,188 predictions from GeneMark
[Jan 06 10:22 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Jan 06 10:48 PM]: 1,108 valid BUSCO predictions found, validating protein sequences
[Jan 06 10:50 PM]: 877 BUSCO predictions validated
[Jan 06 10:50 PM]: Training Augustus using BUSCO gene models
Error: In sequence LG_1_711507-714664: 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 LG_1_806566-809495: 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 LG_1_1341361-1344585: One CDS exon does not begin properly after the previous CDS exon.602 >= 600
GBProcessor::getGeneList(): Intron has non-positive length.
augustus: ERROR
	No genbank sequences found.

Traceback (most recent call last):
  File "/root/miniconda3/envs/funannotate/bin/funannotate", line 10, in <module>
    sys.exit(main())
  File "/root/miniconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/funannotate.py", line 717, in main
    mod.main(arguments)
  File "/root/miniconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/predict.py", line 2094, in main
    lib.trainAugustus(
  File "/root/miniconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/library.py", line 10971, in trainAugustus
    train_results = getTrainResults(
  File "/root/miniconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/library.py", line 10708, in getTrainResults
    float(values1[1]),
UnboundLocalError: local variable 'values1' referenced before assignment

I have the same error, but it did not occur when I ran the same code with other data.

YLhai avatar Jan 07 '25 08:01 YLhai

What is your augustus version that seem to be part of the problem for some people.

hyphaltip avatar Jan 21 '25 17:01 hyphaltip

I'm getting similar errors on a fairly recent conda install of funannotate. When using the following command...

$conda list -e |grep 'augustus'

while in my funannotate environment I get augustus=3.5.0=pl5321heb9362c_5

This seems to be a common problems for many different conda funannotate/augustus installs.

timtimbruno avatar Jan 22 '25 14:01 timtimbruno

I'm getting similar errors on a fairly recent conda install of funannotate. When using the following command...

$conda list -e |grep 'augustus'

while in my funannotate environment I get augustus=3.5.0=pl5321heb9362c_5

This seems to be a common problems for many different conda funannotate/augustus installs.

I have the same augustus build and ran into the same problem today. It looks like I need to try to install a different Augustus.

marinemicrobe avatar Jan 22 '25 15:01 marinemicrobe

I tried lots of things trying to get conda based funannotate to work. The docker image seems to have worked right out of the gate for me and install took a fraction of the time. Hope this helps.

timtimbruno avatar Jan 23 '25 01:01 timtimbruno

I tried lots of things trying to get conda based funannotate to work. The docker image seems to have worked right out of the gate for me and install took a fraction of the time. Hope this helps.

Thanks for the tip! Indeed docker worked for me. Conda install never worked for v1.8.17.

marinemicrobe avatar Jan 23 '25 14:01 marinemicrobe

I solve the problem by recreating the rna-bam file with hisat2.

YLhai avatar Jan 25 '25 04:01 YLhai

I just updated the bioconda recipe. I found that the error goes away if the version of the evidencemodeler requirement is pinned:

https://github.com/bioconda/bioconda-recipes/pull/53985

Also the phyml requirement was missing (also in the Dockerfile here).

bernt-matthias avatar Feb 26 '25 16:02 bernt-matthias