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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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funannotate predict error #674

Open liuyca1 opened 2 years ago

liuyca1 commented 2 years ago

We use the same parameters to predict genes, of which there are two species have the same error when gene prediction

$more funannotate-predict.log [11/30/21 18:36:19]: /opt/anaconda3/envs/funannotate/bin/funannotate predict -i Russula_virescens_genomic_masked.fna --species Russula virescens -o ./fun --busco_seed_species anidulans --buscodb dikarya --min training_models 150 -d /data/liuyuanchao/funannotate_test/alldatabase --cpus 48 --name RVir

[11/30/21 18:36:19]: OS: CentOS Linux 7, 160 cores, ~ 958 GB RAM. Python: 3.9.7 [11/30/21 18:36:19]: Running funannotate v1.8.7 [11/30/21 18:36:19]: GeneMark path: /data/software/gmes_linux_64 [11/30/21 18:36:19]: Full path to gmes_petap.pl: /data/software/gmes_linux_64/gmes_petap.pl [11/30/21 18:36:19]: GeneMark appears to be functional? True [11/30/21 18:36:20]: {'augustus': 1, 'hiq': 2, 'genemark': 1, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1} [11/30/21 18:36:20]: Skipping CodingQuarry as no --rna_bam passed [11/30/21 18:36:20]: {'augustus': 'busco', 'genemark': 'selftraining', 'snap': 'busco', 'glimmerhmm': 'busco'} [11/30/21 18:36:20]: Parsed training data, run ab-initio gene predictors as follows: [11/30/21 18:36:21]: {'augustus': 1, 'hiq': 2, 'genemark': 1, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1} [11/30/21 18:36:42]: Loading genome assembly and parsing soft-masked repetitive sequences [11/30/21 18:37:14]: Genome loaded: 7,382 scaffolds; 64,394,182 bp; 12.49% repeats masked

11/30/21 18:53:42: Running GeneMark-ES on assembly 11/30/21 18:53:42: /data/software/gmes_linux_64/gmes_petap.pl --ES --max_intron 3000 --soft_mask 2000 --cores 48 --sequence /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genom e.softmasked.fa --fungus [11/30/21 19:13:30]: (None, b'') [11/30/21 19:13:31]: perl /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl ./fun/predict_misc/genemark.gff [11/30/21 19:13:36]: 20,537 predictions from GeneMark [11/30/21 19:13:36]: Running BUSCO to find conserved gene models for training ab-initio predictors [11/30/21 19:13:36]: /opt/anaconda3/envs/funannotate/bin/python /opt/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py -i /data/liuyuanchao/funannotate_test/An alysis/Russula_virescens/fun/predict_misc/genome.softmasked.fa -m genome --lineage /data/liuyuanchao/funannotate_test/all_database/dikarya -o russula_virescens -c 48 --species anidulans -f --local_augustus /dat a/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/ab_initio_parameters/augustus [11/30/21 19:18:06]: 1,019 valid BUSCO predictions found, validating protein sequences [11/30/21 19:19:16]: 1,012 BUSCO predictions validated [11/30/21 19:19:16]: Training Augustus using BUSCO gene models [11/30/21 19:19:16]: gff2gbSmallDNA.pl ./fun/predict_misc/busco.final.gff3 /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genome.softmasked.fa 600 ./fun/predict_misc/augustus.tra ining.busco.gb [11/30/21 19:19:32]: Augustus initial training results: [11/30/21 19:19:32]: Accuracy seems low, you can try to improve by passing the --optimize_augustus option. [11/30/21 19:19:32]: Running Augustus gene prediction using russula_virescens parameters [11/30/21 19:25:11]: perl /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl ./fun/predict_misc/augustus.gff3 [11/30/21 19:25:14]: Pulling out high quality Augustus predictions [11/30/21 19:25:14]: Found 8 high quality predictions from Augustus (>90% exon evidence) [11/30/21 19:25:15]: Running SNAP gene prediction, using training data: ./fun/predict_misc/busco.final.gff3 [11/30/21 19:25:15]: 1012 gene models to train snap on 414 scaffolds [11/30/21 19:25:16]: fathom /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/snap.training.zff /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/snap-t raining.scaffolds.fasta -categorize 1000 -min-intron 10 -max-intron 3000 [11/30/21 19:25:17]: fathom uni.ann uni.dna -export 1000 -plus [11/30/21 19:25:17]: forge export.ann export.dna [11/30/21 19:25:18]: perl /opt/anaconda3/envs/funannotate/bin/hmm-assembler.pl snap-trained ./fun/predict_misc/snaptrain [11/30/21 19:25:18]: snap /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/snap-trained.hmm /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genome.so ftmasked.fa [11/30/21 19:29:23]: 1,888 predictions from SNAP [11/30/21 19:29:23]: Running GlimmerHMM gene prediction, using training data: ./fun/predict_misc/busco.final.gff3 [11/30/21 19:29:24]: trainGlimmerHMM /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genome.softmasked.fa /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict _misc/glimmer.exons -d ./fun/predict_misc/glimmerhmm [11/30/21 19:34:00]: perl /opt/anaconda3/envs/funannotate/bin/glimmhmm.pl /opt/anaconda3/envs/funannotate/bin/glimmerhmm /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genome.sof tmasked.fa /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/glimmerhmm -g [11/30/21 19:47:15]: 20,926 predictions from GlimmerHMM [11/30/21 19:47:16]: Prediction sources: ['Augustus', 'HiQ', 'GeneMark', 'GlimmerHMM', 'snap'] [11/30/21 19:47:17]: Summary of gene models: {'total': 55367, 'Augustus': 12008, 'HiQ': 8, 'GeneMark': 20537, 'GlimmerHMM': 20926, 'snap': 1888} [11/30/21 19:47:17]: EVM Weights: {'Augustus': 1, 'HiQ': 2, 'GeneMark': 1, 'GlimmerHMM': 1, 'snap': 1, 'proteins': 1} [11/30/21 19:47:17]: Summary of gene models passed to EVM (weights): [11/30/21 19:47:17]: Launching EVM via funannotate-runEVM.py [11/30/21 19:47:17]: /opt/anaconda3/envs/funannotate/bin/python /opt/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/funannotate-runEVM.py -w /data/liuyuanchao/funannotate_test/An alysis/Russula_virescens/fun/predict_misc/weights.evm.txt -c 48 -g /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/gene_predictions.gff3 -d /data/liuyuanchao/funannotate_test/Anal ysis/Russula_virescens/fun/predict_misc/EVM -f /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genome.softmasked.fa -l ./fun/logfiles/funannotate-EVM.log -m 10 -i 1500 -o /data/li uyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/evm.round1.gff3 --EVM_HOME /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 -p /data/liuyuanchao/funannotate_test/Analysis/Russula _virescens/fun/predict_misc/protein_alignments.gff3 [11/30/21 19:47:22]: Evidence modeler has failed, exiting

$more /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/logfiles/funannotate-predict.log [11/30/21 18:05:06]: /opt/anaconda3/envs/funannotate/bin/funannotate predict -i Bolbitius_vitellinus_genomic_masked.fna --species Bolbitius vitellinus -o ./fun --busco_seed_species anidulans --busco_db dikarya --min_training_models 150 -d /data/liuyuanchao/funannotate_test/alldatabase --cpus 48 --name BVi --transcript_evidence Bolbitius_vitellinus.transcriptome.fasta

[11/30/21 18:05:06]: OS: CentOS Linux 7, 160 cores, ~ 958 GB RAM. Python: 3.9.7 [11/30/21 18:05:06]: Running funannotate v1.8.7 [11/30/21 18:05:06]: GeneMark path: /data/software/gmes_linux_64 [11/30/21 18:05:06]: Full path to gmes_petap.pl: /data/software/gmes_linux_64/gmes_petap.pl [11/30/21 18:05:06]: GeneMark appears to be functional? True [11/30/21 18:05:07]: {'augustus': 1, 'hiq': 2, 'genemark': 1, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1} [11/30/21 18:05:07]: Skipping CodingQuarry as no --rna_bam passed [11/30/21 18:05:07]: {'augustus': 'busco', 'genemark': 'selftraining', 'snap': 'busco', 'glimmerhmm': 'busco'} [11/30/21 18:05:07]: Parsed training data, run ab-initio gene predictors as follows: [11/30/21 18:05:08]: {'augustus': 1, 'hiq': 2, 'genemark': 1, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1} [11/30/21 18:05:18]: Loading genome assembly and parsing soft-masked repetitive sequences [11/30/21 18:05:19]: Genome loaded: 428 scaffolds; 51,241,791 bp; 2.71% repeats masked [11/30/21 18:05:21]: Aligning transcript evidence to genome with minimap2 [11/30/21 18:05:21]: minimap2 -ax splice -t 48 --cs -u b -G 3000 /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa ./fun/predict_misc/transcripts.combine d.fa | samtools sort --reference /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa -@ 4 -o ./fun/predict_misc/transcripts.minimap2.bam - [11/30/21 18:05:43]: Found 70,702 alignments, wrote GFF3 and Augustus hints to file

[11/30/21 18:18:58]: Running GeneMark-ES on assembly [11/30/21 18:18:58]: /data/software/gmes_linux_64/gmes_petap.pl --ES --max_intron 3000 --soft_mask 2000 --cores 48 --sequence /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_mis c/genome.softmasked.fa --fungus [11/30/21 18:33:15]: (None, b'') [11/30/21 18:33:18]: perl /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl ./fun/predict_misc/genemark.gff [11/30/21 18:33:24]: 18,642 predictions from GeneMark [11/30/21 18:33:24]: Running BUSCO to find conserved gene models for training ab-initio predictors [11/30/21 18:33:24]: /opt/anaconda3/envs/funannotate/bin/python /opt/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py -i /data/liuyuanchao/funannotate_test/An alysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa -m genome --lineage /data/liuyuanchao/funannotate_test/all_database/dikarya -o bolbitius_vitellinus -c 48 --species anidulans -f --local_aug ustus /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/ab_initio_parameters/augustus [11/30/21 18:41:42]: 829 valid BUSCO predictions found, validating protein sequences [11/30/21 18:43:08]: 816 BUSCO predictions validated [11/30/21 18:43:08]: Training Augustus using BUSCO gene models [11/30/21 18:43:08]: gff2gbSmallDNA.pl ./fun/predict_misc/busco.final.gff3 /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa 600 ./fun/predict_misc/augus tus.training.busco.gb [11/30/21 18:43:24]: Augustus initial training results: [11/30/21 18:43:24]: Accuracy seems low, you can try to improve by passing the --optimize_augustus option. [11/30/21 18:43:24]: Running Augustus gene prediction using bolbitius_vitellinus parameters [11/30/21 18:45:20]: perl /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl ./fun/predict_misc/augustus.gff3 [11/30/21 18:45:25]: Pulling out high quality Augustus predictions [11/30/21 18:45:26]: Found 1,907 high quality predictions from Augustus (>90% exon evidence) [11/30/21 18:45:26]: Running SNAP gene prediction, using training data: ./fun/predict_misc/busco.final.gff3 [11/30/21 18:45:27]: 816 gene models to train snap on 55 scaffolds [11/30/21 18:45:27]: fathom /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/snap.training.zff /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predi ct_misc/snap-training.scaffolds.fasta -categorize 1000 -min-intron 10 -max-intron 3000 [11/30/21 18:45:29]: fathom uni.ann uni.dna -export 1000 -plus [11/30/21 18:45:30]: forge export.ann export.dna [11/30/21 18:45:30]: perl /opt/anaconda3/envs/funannotate/bin/hmm-assembler.pl snap-trained ./fun/predict_misc/snaptrain [11/30/21 18:45:30]: snap /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/snap-trained.hmm /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinusJGI/fun/predict misc/genome.softmasked.fa [11/30/21 18:49:26]: 475 predictions from SNAP [11/30/21 18:49:26]: Running GlimmerHMM gene prediction, using training data: ./fun/predict_misc/busco.final.gff3 [11/30/21 18:49:27]: trainGlimmerHMM /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_J GI/fun/predict_misc/glimmer.exons -d ./fun/predict_misc/glimmerhmm [11/30/21 18:55:32]: perl /opt/anaconda3/envs/funannotate/bin/glimmhmm.pl /opt/anaconda3/envs/funannotate/bin/glimmerhmm /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/gen ome.softmasked.fa /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/glimmerhmm -g [11/30/21 19:04:31]: 16,560 predictions from GlimmerHMM [11/30/21 19:04:31]: Prediction sources: ['Augustus', 'HiQ', 'GeneMark', 'GlimmerHMM', 'snap'] [11/30/21 19:04:32]: Summary of gene models: {'total': 50255, 'Augustus': 12671, 'HiQ': 1907, 'GeneMark': 18642, 'GlimmerHMM': 16560, 'snap': 475} [11/30/21 19:04:32]: EVM Weights: {'Augustus': 1, 'HiQ': 2, 'GeneMark': 1, 'GlimmerHMM': 1, 'snap': 1, 'proteins': 1, 'transcripts': 1} [11/30/21 19:04:32]: Summary of gene models passed to EVM (weights): [11/30/21 19:04:32]: Launching EVM via funannotate-runEVM.py [11/30/21 19:04:32]: /opt/anaconda3/envs/funannotate/bin/python /opt/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/funannotate-runEVM.py -w /data/liuyuanchao/funannotate_test/An alysis/Bolbitius_vitellinus_JGI/fun/predict_misc/weights.evm.txt -c 48 -g /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/gene_predictions.gff3 -d /data/liuyuanchao/funanno tate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/EVM -f /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa -l ./fun/logfiles/funannotate-EVM.l og -m 10 -i 1500 -o /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/evm.round1.gff3 --EVM_HOME /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 -p /data/liuyuancha o/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/protein_alignments.gff3 -t /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/transcript_alignments.gff3 [11/30/21 19:04:37]: Evidence modeler has failed, exiting

nextgenusfs commented 2 years ago

In the logfiles folder is a funannotate-EVM.log file, can you post the output of that?

nextgenusfs commented 2 years ago

It is most likely an error in the EvidenceModeler partitioning scheme that was fixed in v1.8.9 -- looks like you are running v1.8.7 here.

liuyca1 commented 2 years ago

In the logfiles folder is a funannotate-EVM.log file, can you post the output of that?

ok, what is the email address?

liuyca1 commented 2 years ago

cd

In the logfiles folder is a funannotate-EVM.log file, can you post the output of that?

[11/30/21 19:04:32]: /opt/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/funannotate-runEVM.py -w /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/weights.evm.txt -c 48 -g /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/gene_predictions.gff3 -d /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/EVM -f /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/genome.softmasked.fa -l ./fun/logfiles/funannotate-EVM.log -m 10 -i 1500 -o /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/evm.round1.gff3 --EVM_HOME /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 -p /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/protein_alignments.gff3 -t /data/liuyuanchao/funannotate_test/Analysis/Bolbitius_vitellinus_JGI/fun/predict_misc/transcript_alignments.gff3

[11/30/21 19:04:32]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval [11/30/21 19:04:36]: 428 total contigs; skipping 2 contigs with no genes [11/30/21 19:04:36]: Merged 50255 genes into 15155 supergenes with bedtools [11/30/21 19:04:36]: BVi.1_1-123400 --> 123399 bp [11/30/21 19:04:36]: BVi.1_121754-223238 --> 101484 bp [11/30/21 19:04:36]: BVi.1_220702-353129 --> 132427 bp [11/30/21 19:04:36]: BVi.1_347100-495175 --> 148075 bp [11/30/21 19:04:36]: BVi.1_493292-563645 --> 70353 bp [11/30/21 19:04:36]: BVi.1_561814-630265 --> 68451 bp [11/30/21 19:04:36]: BVi.1_628123-772035 --> 143912 bp [11/30/21 19:04:36]: BVi.1_770079-869670 --> 99591 bp [11/30/21 19:04:36]: BVi.1_861951-952892 --> 90941 bp [11/30/21 19:04:36]: BVi.1_950402-1012444 --> 62042 bp [11/30/21 19:04:36]: BVi.1_1009925-1275255 --> 265330 bp [11/30/21 19:04:36]: BVi.1_1273092-1465245 --> 192153 bp [11/30/21 19:04:36]: BVi.1_1463034-1604140 --> 141106 bp [11/30/21 19:04:36]: BVi.1_1595787-1884957 --> 289170 bp [11/30/21 19:04:36]: BVi.1_1882397-1986504 --> 104107 bp [11/30/21 19:04:36]: BVi.1_1984486-2034977 --> 50491 bp [11/30/21 19:04:36]: BVi.1_2031675-2181582 --> 149907 bp [11/30/21 19:04:36]: BVi.1_2179162-2257158 --> 77996 bp [11/30/21 19:04:36]: BVi.1_2255543-2375158 --> 119615 bp [11/30/21 19:04:36]: BVi.1_2372952-2494044 --> 121092 bp [11/30/21 19:04:36]: BVi.1_2491905-2507717 --> 15812 bp [11/30/21 19:04:36]: BVi.1_2504715-2704086 --> 199371 bp [11/30/21 19:04:36]: BVi.1_2701059-2813377 --> 112318 bp [11/30/21 19:04:36]: BVi.1_2810096-2918161 --> 108065 bp [11/30/21 19:04:36]: BVi.2_1-44371 --> 44370 bp [11/30/21 19:04:36]: BVi.2_42866-181672 --> 138806 bp [11/30/21 19:04:36]: BVi.2_180124-282779 --> 102655 bp [11/30/21 19:04:36]: BVi.2_281186-324556 --> 43370 bp [11/30/21 19:04:36]: BVi.2_322171-498858 --> 176687 bp [11/30/21 19:04:36]: BVi.2_497070-574566 --> 77496 bp [11/30/21 19:04:36]: BVi.2_569905-611779 --> 41874 bp [11/30/21 19:04:36]: BVi.2_609789-751300 --> 141511 bp [11/30/21 19:04:36]: BVi.2_749640-1014079 --> 264439 bp [11/30/21 19:04:36]: BVi.2_1011253-1037358 --> 26105 bp [11/30/21 19:04:36]: BVi.2_1034696-1166267 --> 131571 bp [11/30/21 19:04:36]: BVi.2_1156822-1282410 --> 125588 bp [11/30/21 19:04:36]: BVi.2_1280201-1580748 --> 300547 bp [11/30/21 19:04:36]: BVi.2_1578465-1731819 --> 153354 bp [11/30/21 19:04:36]: BVi.2_1719608-1800022 --> 80414 bp [11/30/21 19:04:36]: BVi.2_1798491-1930967 --> 132476 bp [11/30/21 19:04:36]: BVi.2_1928927-2040402 --> 111475 bp [11/30/21 19:04:36]: BVi.2_2037453-2182527 --> 145074 bp [11/30/21 19:04:36]: BVi.2_2180660-2256508 --> 75848 bp [11/30/21 19:04:36]: BVi.2_2254249-2384424 --> 130175 bp [11/30/21 19:04:36]: BVi.2_2382472-2523468 --> 140996 bp [11/30/21 19:04:36]: BVi.2_2521816-2608693 --> 86877 bp [11/30/21 19:04:36]: BVi.3_1-78388 --> 78387 bp [11/30/21 19:04:36]: BVi.3_76634-180628 --> 103994 bp [11/30/21 19:04:36]: BVi.3_177297-296713 --> 119416 bp [11/30/21 19:04:36]: BVi.3_292035-393206 --> 101171 bp [11/30/21 19:04:36]: BVi.3_390989-461745 --> 70756 bp [11/30/21 19:04:36]: BVi.3_457178-592977 --> 135799 bp [11/30/21 19:04:36]: BVi.3_591220-704701 --> 113481 bp [11/30/21 19:04:36]: BVi.3_703161-774044 --> 70883 bp [11/30/21 19:04:36]: BVi.3_771988-840481 --> 68493 bp [11/30/21 19:04:36]: BVi.3_836912-991987 --> 155075 bp [11/30/21 19:04:36]: BVi.3_990080-1095806 --> 105726 bp [11/30/21 19:04:36]: BVi.3_1094209-1188977 --> 94768 bp [11/30/21 19:04:36]: BVi.3_1186837-1292566 --> 105729 bp [11/30/21 19:04:36]: BVi.3_1290265-1416867 --> 126602 bp [11/30/21 19:04:36]: BVi.3_1415008-1437586 --> 22578 bp [11/30/21 19:04:36]: BVi.3_1435256-1583917 --> 148661 bp [11/30/21 19:04:36]: BVi.3_1582098-1723388 --> 141290 bp [11/30/21 19:04:36]: BVi.3_1721638-1843925 --> 122287 bp [11/30/21 19:04:36]: BVi.3_1841932-1929295 --> 87363 bp [11/30/21 19:04:36]: BVi.3_1927766-2064443 --> 136677 bp [11/30/21 19:04:36]: BVi.3_2062304-2176294 --> 113990 bp [11/30/21 19:04:36]: BVi.4_1-135023 --> 135022 bp [11/30/21 19:04:36]: BVi.4_131230-175410 --> 44180 bp [11/30/21 19:04:36]: BVi.4_173427-348801 --> 175374 bp [11/30/21 19:04:36]: BVi.4_346739-425738 --> 78999 bp [11/30/21 19:04:36]: BVi.4_419819-553965 --> 134146 bp [11/30/21 19:04:36]: BVi.4_552247-679834 --> 127587 bp [11/30/21 19:04:36]: BVi.4_677767-771488 --> 93721 bp [11/30/21 19:04:36]: BVi.4_766497-863308 --> 96811 bp [11/30/21 19:04:36]: BVi.4_859109-933505 --> 74396 bp [11/30/21 19:04:36]: BVi.4_931707-1068770 --> 137063 bp [11/30/21 19:04:36]: BVi.4_1066980-1178338 --> 111358 bp [11/30/21 19:04:36]: BVi.4_1176601-1292047 --> 115446 bp [11/30/21 19:04:36]: BVi.4_1287892-1444999 --> 157107 bp [11/30/21 19:04:36]: BVi.4_1441700-1533101 --> 91401 bp [11/30/21 19:04:36]: BVi.4_1531390-1728837 --> 197447 bp [11/30/21 19:04:36]: BVi.4_1719248-1875001 --> 155753 bp [11/30/21 19:04:36]: BVi.5_1-126215 --> 126214 bp [11/30/21 19:04:36]: BVi.5_124416-237970 --> 113554 bp [11/30/21 19:04:36]: BVi.5_236259-368911 --> 132652 bp [11/30/21 19:04:36]: BVi.5_365849-494925 --> 129076 bp [11/30/21 19:04:36]: BVi.5_493189-577449 --> 84260 bp [11/30/21 19:04:36]: BVi.5_575009-679600 --> 104591 bp [11/30/21 19:04:36]: BVi.5_676895-786227 --> 109332 bp [11/30/21 19:04:36]: BVi.5_784557-887809 --> 103252 bp [11/30/21 19:04:36]: BVi.5_884623-993484 --> 108861 bp [11/30/21 19:04:36]: BVi.5_990873-1110120 --> 119247 bp [11/30/21 19:04:36]: BVi.5_1107542-1201082 --> 93540 bp [11/30/21 19:04:36]: BVi.5_1197600-1318459 --> 120859 bp [11/30/21 19:04:36]: BVi.5_1316289-1457003 --> 140714 bp [11/30/21 19:04:36]: BVi.5_1455271-1572957 --> 117686 bp [11/30/21 19:04:36]: BVi.6_1-91486 --> 91485 bp [11/30/21 19:04:36]: BVi.6_89650-220947 --> 131297 bp [11/30/21 19:04:36]: BVi.6_218321-324353 --> 106032 bp [11/30/21 19:04:36]: BVi.6_321007-428542 --> 107535 bp [11/30/21 19:04:36]: BVi.6_421960-583252 --> 161292 bp [11/30/21 19:04:36]: BVi.6_581693-724819 --> 143126 bp [11/30/21 19:04:36]: BVi.6_723282-834212 --> 110930 bp [11/30/21 19:04:36]: BVi.6_832338-985027 --> 152689 bp [11/30/21 19:04:36]: BVi.6_983476-1089208 --> 105732 bp [11/30/21 19:04:36]: BVi.6_1084163-1185926 --> 101763 bp [11/30/21 19:04:36]: BVi.6_1184191-1290577 --> 106386 bp [11/30/21 19:04:36]: BVi.6_1287256-1350701 --> 63445 bp [11/30/21 19:04:36]: BVi.6_1348078-1497109 --> 149031 bp [11/30/21 19:04:36]: BVi.7_1-72252 --> 72251 bp [11/30/21 19:04:36]: BVi.7_68566-358501 --> 289935 bp [11/30/21 19:04:36]: BVi.7_356054-563052 --> 206998 bp [11/30/21 19:04:36]: BVi.7_559415-644528 --> 85113 bp [11/30/21 19:04:36]: BVi.7_642119-745916 --> 103797 bp [11/30/21 19:04:36]: BVi.7_744267-834459 --> 90192 bp [11/30/21 19:04:36]: BVi.7_830361-927398 --> 97037 bp [11/30/21 19:04:36]: BVi.7_925210-1077173 --> 151963 bp [11/30/21 19:04:36]: BVi.7_1075427-1216082 --> 140655 bp [11/30/21 19:04:36]: BVi.7_1213656-1346819 --> 133163 bp [11/30/21 19:04:36]: BVi.8_1-79449 --> 79448 bp [11/30/21 19:04:36]: BVi.8_74666-202264 --> 127598 bp [11/30/21 19:04:36]: BVi.8_196117-338224 --> 142107 bp [11/30/21 19:04:36]: BVi.8_336386-640301 --> 303915 bp [11/30/21 19:04:36]: BVi.8_637688-699283 --> 61595 bp [11/30/21 19:04:36]: BVi.8_696700-821279 --> 124579 bp [11/30/21 19:04:36]: BVi.8_816561-874469 --> 57908 bp [11/30/21 19:04:36]: BVi.8_872839-1037115 --> 164276 bp [11/30/21 19:04:36]: BVi.8_1034784-1110302 --> 75518 bp [11/30/21 19:04:36]: BVi.8_1107749-1227864 --> 120115 bp [11/30/21 19:04:36]: BVi.9_1-30785 --> 30784 bp [11/30/21 19:04:36]: BVi.9_27167-172115 --> 144948 bp [11/30/21 19:04:36]: BVi.9_169509-318973 --> 149464 bp [11/30/21 19:04:36]: BVi.9_312469-431101 --> 118632 bp [11/30/21 19:04:36]: BVi.9_429077-519821 --> 90744 bp [11/30/21 19:04:36]: BVi.9_517396-576097 --> 58701 bp [11/30/21 19:04:36]: BVi.9_574584-688108 --> 113524 bp [11/30/21 19:04:36]: BVi.9_685649-817959 --> 132310 bp [11/30/21 19:04:36]: BVi.9_815329-923403 --> 108074 bp [11/30/21 19:04:36]: BVi.9_920393-1027840 --> 107447 bp [11/30/21 19:04:36]: BVi.9_1025829-1133050 --> 107221 bp [11/30/21 19:04:36]: BVi.10_1-114941 --> 114940 bp [11/30/21 19:04:36]: BVi.10_113268-229386 --> 116118 bp [11/30/21 19:04:36]: BVi.10_226368-323023 --> 96655 bp [11/30/21 19:04:36]: BVi.10_321446-430594 --> 109148 bp [11/30/21 19:04:36]: BVi.10_427662-552220 --> 124558 bp [11/30/21 19:04:36]: BVi.10_549968-674835 --> 124867 bp [11/30/21 19:04:36]: BVi.10_672998-767623 --> 94625 bp [11/30/21 19:04:36]: BVi.10_765648-927485 --> 161837 bp [11/30/21 19:04:36]: BVi.10_925393-1063304 --> 137911 bp [11/30/21 19:04:36]: BVi.11_1-149471 --> 149470 bp [11/30/21 19:04:36]: BVi.11_147808-333624 --> 185816 bp [11/30/21 19:04:36]: BVi.11_328586-466069 --> 137483 bp [11/30/21 19:04:36]: BVi.11_463863-560147 --> 96284 bp [11/30/21 19:04:36]: BVi.11_557338-650869 --> 93531 bp [11/30/21 19:04:36]: BVi.11_649334-756835 --> 107501 bp [11/30/21 19:04:36]: BVi.11_755008-847756 --> 92748 bp [11/30/21 19:04:36]: BVi.11_843876-956406 --> 112530 bp [11/30/21 19:04:36]: BVi.12_1-95907 --> 95906 bp [11/30/21 19:04:36]: BVi.12_87958-166292 --> 78334 bp [11/30/21 19:04:36]: BVi.12_160238-470448 --> 310210 bp [11/30/21 19:04:36]: BVi.12_468190-559201 --> 91011 bp [11/30/21 19:04:36]: BVi.12_553860-657135 --> 103275 bp [11/30/21 19:04:36]: BVi.12_654718-672380 --> 17662 bp [11/30/21 19:04:36]: BVi.12_670650-851059 --> 180409 bp [11/30/21 19:04:36]: BVi.12_848978-945712 --> 96734 bp [11/30/21 19:04:36]: BVi.13_1-82320 --> 82319 bp [11/30/21 19:04:36]: BVi.13_79150-146739 --> 67589 bp [11/30/21 19:04:36]: BVi.13_144788-308659 --> 163871 bp [11/30/21 19:04:36]: BVi.13_307021-391766 --> 84745 bp [11/30/21 19:04:36]: BVi.13_389454-518494 --> 129040 bp [11/30/21 19:04:36]: BVi.13_516333-621666 --> 105333 bp [11/30/21 19:04:36]: BVi.13_619488-685293 --> 65805 bp [11/30/21 19:04:36]: BVi.13_682874-799676 --> 116802 bp [11/30/21 19:04:37]: BVi.13_794596-906897 --> 112301 bp [11/30/21 19:04:37]: BVi.14_1-99585 --> 99584 bp [11/30/21 19:04:37]: BVi.14_97304-207566 --> 110262 bp [11/30/21 19:04:37]: BVi.14_205408-322481 --> 117073 bp [11/30/21 19:04:37]: BVi.14_320429-434322 --> 113893 bp [11/30/21 19:04:37]: BVi.14_431631-525696 --> 94065 bp [11/30/21 19:04:37]: BVi.14_524038-629736 --> 105698 bp [11/30/21 19:04:37]: BVi.14_628088-742346 --> 114258 bp [11/30/21 19:04:37]: BVi.14_740429-895854 --> 155425 bp [11/30/21 19:04:37]: BVi.15_1-120292 --> 120291 bp [11/30/21 19:04:37]: BVi.15_118592-225475 --> 106883 bp [11/30/21 19:04:37]: BVi.15_223505-334110 --> 110605 bp [11/30/21 19:04:37]: BVi.15_332256-449098 --> 116842 bp [11/30/21 19:04:37]: BVi.15_444343-562079 --> 117736 bp [11/30/21 19:04:37]: BVi.15_560569-640087 --> 79518 bp [11/30/21 19:04:37]: BVi.15_638347-732615 --> 94268 bp [11/30/21 19:04:37]: BVi.15_725595-852468 --> 126873 bp [11/30/21 19:04:37]: BVi.16_1-77229 --> 77228 bp [11/30/21 19:04:37]: BVi.16_75403-185112 --> 109709 bp [11/30/21 19:04:37]: BVi.16_181252-268735 --> 87483 bp [11/30/21 19:04:37]: BVi.16_267096-361676 --> 94580 bp [11/30/21 19:04:37]: BVi.16_359926-442432 --> 82506 bp [11/30/21 19:04:37]: BVi.16_440263-561775 --> 121512 bp [11/30/21 19:04:37]: BVi.16_559839-600461 --> 40622 bp [11/30/21 19:04:37]: BVi.16_598791-784555 --> 185764 bp [11/30/21 19:04:37]: BVi.17_1-65252 --> 65251 bp [11/30/21 19:04:37]: BVi.17_63605-213607 --> 150002 bp [11/30/21 19:04:37]: BVi.17_211752-281528 --> 69776 bp [11/30/21 19:04:37]: BVi.17_279553-390171 --> 110618 bp [11/30/21 19:04:37]: BVi.17_388660-475385 --> 86725 bp [11/30/21 19:04:37]: BVi.17_473535-594905 --> 121370 bp [11/30/21 19:04:37]: BVi.17_592562-735728 --> 143166 bp [11/30/21 19:04:37]: BVi.18_1-71179 --> 71178 bp [11/30/21 19:04:37]: BVi.18_69523-249692 --> 180169 bp [11/30/21 19:04:37]: BVi.18_248194-343983 --> 95789 bp [11/30/21 19:04:37]: BVi.18_342419-508574 --> 166155 bp [11/30/21 19:04:37]: BVi.18_505720-726277 --> 220557 bp [11/30/21 19:04:37]: BVi.19_1-76956 --> 76955 bp [11/30/21 19:04:37]: BVi.19_73100-221768 --> 148668 bp [11/30/21 19:04:37]: BVi.19_219551-331911 --> 112360 bp [11/30/21 19:04:37]: BVi.19_330021-479457 --> 149436 bp [11/30/21 19:04:37]: BVi.19_476474-576143 --> 99669 bp [11/30/21 19:04:37]: BVi.19_571774-714194 --> 142420 bp [11/30/21 19:04:37]: BVi.20_1-177395 --> 177394 bp [11/30/21 19:04:37]: BVi.20_171611-288048 --> 116437 bp [11/30/21 19:04:37]: BVi.20_283875-413097 --> 129222 bp [11/30/21 19:04:37]: BVi.20_411243-508433 --> 97190 bp [11/30/21 19:04:37]: BVi.20_506811-597543 --> 90732 bp [11/30/21 19:04:37]: BVi.20_593263-696705 --> 103442 bp [11/30/21 19:04:37]: BVi.21_1-103078 --> 103077 bp [11/30/21 19:04:37]: BVi.21_101410-195713 --> 94303 bp [11/30/21 19:04:37]: BVi.21_191633-346278 --> 154645 bp [11/30/21 19:04:37]: BVi.21_344725-444030 --> 99305 bp [11/30/21 19:04:37]: BVi.21_442265-551534 --> 109269 bp [11/30/21 19:04:37]: BVi.21_547805-675891 --> 128086 bp [11/30/21 19:04:37]: BVi.22_1-90690 --> 90689 bp [11/30/21 19:04:37]: BVi.22_88969-232362 --> 143393 bp [11/30/21 19:04:37]: BVi.22_228354-322228 --> 93874 bp [11/30/21 19:04:37]: BVi.22_320706-437692 --> 116986 bp [11/30/21 19:04:37]: BVi.22_433707-544025 --> 110318 bp [11/30/21 19:04:37]: BVi.22_541284-641256 --> 99972 bp [11/30/21 19:04:37]: BVi.23_1-68211 --> 68210 bp [11/30/21 19:04:37]: BVi.23_63989-270350 --> 206361 bp [11/30/21 19:04:37]: BVi.23_267122-300903 --> 33781 bp [11/30/21 19:04:37]: BVi.23_298213-431372 --> 133159 bp [11/30/21 19:04:37]: BVi.23_429833-440648 --> 10815 bp [11/30/21 19:04:37]: BVi.23_439080-621835 --> 182755 bp [11/30/21 19:04:37]: BVi.24_1-91404 --> 91403 bp [11/30/21 19:04:37]: BVi.24_89218-194429 --> 105211 bp [11/30/21 19:04:37]: BVi.24_192389-317051 --> 124662 bp [11/30/21 19:04:37]: BVi.24_314747-352405 --> 37658 bp [11/30/21 19:04:37]: BVi.24_349335-466973 --> 117638 bp [11/30/21 19:04:37]: BVi.24_465326-580451 --> 115125 bp [11/30/21 19:04:37]: BVi.25_1-80210 --> 80209 bp [11/30/21 19:04:37]: BVi.25_78297-178808 --> 100511 bp [11/30/21 19:04:37]: BVi.25_175896-372915 --> 197019 bp [11/30/21 19:04:37]: BVi.25_367921-499941 --> 132020 bp [11/30/21 19:04:37]: BVi.26_1-119330 --> 119329 bp [11/30/21 19:04:37]: BVi.26_117518-242648 --> 125130 bp [11/30/21 19:04:37]: BVi.26_238712-367594 --> 128882 bp [11/30/21 19:04:37]: BVi.26_366086-469142 --> 103056 bp [11/30/21 19:04:37]: BVi.27_1-124411 --> 124410 bp [11/30/21 19:04:37]: BVi.27_122534-230493 --> 107959 bp [11/30/21 19:04:37]: BVi.27_227291-364268 --> 136977 bp [11/30/21 19:04:37]: BVi.27_361881-464881 --> 103000 bp [11/30/21 19:04:37]: BVi.28_1-213008 --> 213007 bp [11/30/21 19:04:37]: BVi.28_210735-325818 --> 115083 bp [11/30/21 19:04:37]: BVi.28_323163-437995 --> 114832 bp [11/30/21 19:04:37]: BVi.29_1-147017 --> 147016 bp [11/30/21 19:04:37]: BVi.29_144602-230202 --> 85600 bp [11/30/21 19:04:37]: BVi.29_228527-315404 --> 86877 bp [11/30/21 19:04:37]: BVi.29_313245-397377 --> 84132 bp [11/30/21 19:04:37]: BVi.30_1-101702 --> 101701 bp [11/30/21 19:04:37]: BVi.30_98510-189703 --> 91193 bp [11/30/21 19:04:37]: BVi.30_188087-359357 --> 171270 bp [11/30/21 19:04:37]: BVi.31_1-114571 --> 114570 bp [11/30/21 19:04:37]: BVi.31_112985-217210 --> 104225 bp [11/30/21 19:04:37]: BVi.31_215457-342289 --> 126832 bp [11/30/21 19:04:37]: BVi.32_1-56543 --> 56542 bp [11/30/21 19:04:37]: BVi.32_54498-118070 --> 63572 bp [11/30/21 19:04:37]: BVi.32_116344-259233 --> 142889 bp [11/30/21 19:04:37]: BVi.32_256100-336992 --> 80892 bp [11/30/21 19:04:37]: BVi.33_1-85721 --> 85720 bp [11/30/21 19:04:37]: BVi.33_83891-151772 --> 67881 bp [11/30/21 19:04:37]: BVi.33_149915-252973 --> 103058 bp [11/30/21 19:04:37]: BVi.33_251404-335719 --> 84315 bp [11/30/21 19:04:37]: BVi.34_1-89593 --> 89592 bp [11/30/21 19:04:37]: BVi.34_87992-200928 --> 112936 bp [11/30/21 19:04:37]: BVi.34_198957-334821 --> 135864 bp [11/30/21 19:04:37]: BVi.35_1-71906 --> 71905 bp [11/30/21 19:04:37]: BVi.35_69812-154785 --> 84973 bp [11/30/21 19:04:37]: BVi.35_153170-234691 --> 81521 bp [11/30/21 19:04:37]: BVi.36_1-124905 --> 124904 bp [11/30/21 19:04:37]: BVi.36_121173-209498 --> 88325 bp [11/30/21 19:04:37]: BVi.37_1-109559 --> 109558 bp [11/30/21 19:04:37]: BVi.37_107745-196590 --> 88845 bp [11/30/21 19:04:37]: BVi.38_1-44560 --> 44559 bp [11/30/21 19:04:37]: BVi.38_31554-188630 --> 157076 bp [11/30/21 19:04:37]: BVi.39_1-65921 --> 65920 bp [11/30/21 19:04:37]: BVi.39_64064-186191 --> 122127 bp [11/30/21 19:04:37]: BVi.40_1-77030 --> 77029 bp [11/30/21 19:04:37]: BVi.40_75189-183895 --> 108706 bp [11/30/21 19:04:37]: BVi.41_1-82495 --> 82494 bp [11/30/21 19:04:37]: BVi.41_80430-183556 --> 103126 bp [11/30/21 19:04:37]: BVi.42_1-85026 --> 85025 bp [11/30/21 19:04:37]: BVi.42_83336-177468 --> 94132 bp [11/30/21 19:04:37]: BVi.43_1-54965 --> 54964 bp [11/30/21 19:04:37]: BVi.43_53398-174977 --> 121579 bp [11/30/21 19:04:37]: BVi.44 --> 166125 bp [11/30/21 19:04:37]: BVi.45_1-84887 --> 84886 bp [11/30/21 19:04:37]: BVi.45_83220-158985 --> 75765 bp [11/30/21 19:04:37]: BVi.46_1-50307 --> 50306 bp [11/30/21 19:04:37]: BVi.46_48295-153626 --> 105331 bp [11/30/21 19:04:37]: BVi.47_1-75286 --> 75285 bp [11/30/21 19:04:37]: BVi.47_73308-143927 --> 70619 bp [11/30/21 19:04:37]: BVi.48_1-81248 --> 81247 bp [11/30/21 19:04:37]: BVi.48_78504-142769 --> 64265 bp [11/30/21 19:04:37]: BVi.49_1-59327 --> 59326 bp [11/30/21 19:04:37]: BVi.49_56064-141980 --> 85916 bp [11/30/21 19:04:37]: BVi.50 --> 139946 bp [11/30/21 19:04:37]: BVi.51 --> 134890 bp [11/30/21 19:04:37]: BVi.52 --> 133678 bp

[11/30/21 19:47:18]: /opt/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/aux_scripts/funannotate-runEVM.py -w /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/weights.evm.txt -c 48 -g /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/gene_predictions.gff3 -d /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/EVM -f /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/genome.softmasked.fa -l ./fun/logfiles/funannotate-EVM.log -m 10 -i 1500 -o /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/evm.round1.gff3 --EVM_HOME /opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 -p /data/liuyuanchao/funannotate_test/Analysis/Russula_virescens/fun/predict_misc/protein_alignments.gff3

[11/30/21 19:47:18]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval [11/30/21 19:47:21]: 7,382 total contigs; skipping 1,998 contigs with no genes [11/30/21 19:47:21]: Merged 55367 genes into 20970 supergenes with bedtools [11/30/21 19:47:22]: RVir.1 --> 21951 bp [11/30/21 19:47:22]: RVir.2 --> 2772 bp [11/30/21 19:47:22]: RVir.3 --> 23629 bp [11/30/21 19:47:22]: RVir.4 --> 47633 bp [11/30/21 19:47:22]: RVir.5 --> 7892 bp [11/30/21 19:47:22]: RVir.6 --> 46690 bp [11/30/21 19:47:22]: RVir.7 --> 78630 bp [11/30/21 19:47:22]: RVir.8 --> 2940 bp [11/30/21 19:47:22]: RVir.9_1-106520 --> 106519 bp [11/30/21 19:47:22]: RVir.9_104968-239172 --> 134204 bp [11/30/21 19:47:22]: RVir.9_236068-358942 --> 122874 bp [11/30/21 19:47:22]: RVir.10_1-86317 --> 86316 bp [11/30/21 19:47:22]: RVir.10_82701-218379 --> 135678 bp [11/30/21 19:47:22]: RVir.11 --> 6331 bp [11/30/21 19:47:22]: RVir.12 --> 61663 bp [11/30/21 19:47:22]: RVir.13 --> 4136 bp [11/30/21 19:47:22]: RVir.15 --> 3709 bp [11/30/21 19:47:22]: RVir.16 --> 19433 bp [11/30/21 19:47:22]: RVir.17 --> 2061 bp [11/30/21 19:47:22]: RVir.18 --> 36323 bp [11/30/21 19:47:22]: RVir.19 --> 677 bp [11/30/21 19:47:22]: RVir.20 --> 8452 bp [11/30/21 19:47:22]: RVir.21 --> 2947 bp [11/30/21 19:47:22]: RVir.22 --> 7938 bp [11/30/21 19:47:22]: RVir.23 --> 46733 bp [11/30/21 19:47:22]: RVir.24 --> 100703 bp [11/30/21 19:47:22]: RVir.25 --> 3563 bp [11/30/21 19:47:22]: RVir.26 --> 930 bp [11/30/21 19:47:22]: RVir.27 --> 50795 bp [11/30/21 19:47:22]: RVir.29 --> 4113 bp [11/30/21 19:47:22]: RVir.30 --> 1009 bp [11/30/21 19:47:22]: RVir.31 --> 35563 bp [11/30/21 19:47:22]: RVir.33 --> 1846 bp [11/30/21 19:47:22]: RVir.35 --> 2338 bp [11/30/21 19:47:22]: RVir.36 --> 6175 bp [11/30/21 19:47:22]: RVir.37 --> 11551 bp [11/30/21 19:47:22]: RVir.38 --> 96616 bp [11/30/21 19:47:22]: RVir.39 --> 69203 bp [11/30/21 19:47:22]: RVir.40 --> 32109 bp [11/30/21 19:47:22]: RVir.41 --> 1452 bp [11/30/21 19:47:22]: RVir.42 --> 67632 bp [11/30/21 19:47:22]: RVir.43 --> 6118 bp [11/30/21 19:47:22]: RVir.44 --> 2885 bp [11/30/21 19:47:22]: RVir.45 --> 96516 bp [11/30/21 19:47:22]: RVir.46 --> 19530 bp [11/30/21 19:47:22]: RVir.47 --> 44207 bp [11/30/21 19:47:22]: RVir.48 --> 9027 bp [11/30/21 19:47:22]: RVir.50 --> 7340 bp [11/30/21 19:47:22]: RVir.51 --> 1658 bp [11/30/21 19:47:22]: RVir.52 --> 3382 bp [11/30/21 19:47:22]: RVir.53 --> 1304 bp [11/30/21 19:47:22]: RVir.54 --> 4194 bp [11/30/21 19:47:22]: RVir.55 --> 7615 bp [11/30/21 19:47:22]: RVir.56 --> 47273 bp [11/30/21 19:47:22]: RVir.57 --> 34626 bp [11/30/21 19:47:22]: RVir.58 --> 679 bp [11/30/21 19:47:22]: RVir.59 --> 713 bp [11/30/21 19:47:22]: RVir.60 --> 6110 bp [11/30/21 19:47:22]: RVir.61 --> 22891 bp [11/30/21 19:47:22]: RVir.62 --> 115876 bp [11/30/21 19:47:22]: RVir.64 --> 8488 bp [11/30/21 19:47:22]: RVir.65 --> 85664 bp [11/30/21 19:47:22]: RVir.66 --> 4543 bp [11/30/21 19:47:22]: RVir.67 --> 48711 bp [11/30/21 19:47:22]: RVir.68 --> 40514 bp [11/30/21 19:47:22]: RVir.69 --> 31123 bp [11/30/21 19:47:22]: RVir.70 --> 2919 bp [11/30/21 19:47:22]: RVir.72 --> 1799 bp [11/30/21 19:47:22]: RVir.73 --> 113828 bp [11/30/21 19:47:22]: RVir.74 --> 68307 bp [11/30/21 19:47:22]: RVir.75 --> 41538 bp [11/30/21 19:47:22]: RVir.76 --> 8336 bp [11/30/21 19:47:22]: RVir.77 --> 34326 bp [11/30/21 19:47:22]: RVir.78 --> 7998 bp [11/30/21 19:47:22]: RVir.79 --> 11758 bp [11/30/21 19:47:22]: RVir.80 --> 45801 bp [11/30/21 19:47:22]: RVir.81 --> 72503 bp [11/30/21 19:47:22]: RVir.82 --> 47391 bp [11/30/21 19:47:22]: RVir.83 --> 7617 bp [11/30/21 19:47:22]: RVir.85 --> 46291 bp [11/30/21 19:47:22]: RVir.86 --> 4020 bp [11/30/21 19:47:22]: RVir.87 --> 19822 bp [11/30/21 19:47:22]: RVir.88 --> 37955 bp [11/30/21 19:47:22]: RVir.89 --> 5978 bp

nextgenusfs commented 2 years ago

I don't see anything obvious from this logfile as to why it failed. My suggestion is to upgrade funannotate as I don't have time to troubleshoot older versions.