[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H0297.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H00RI.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H002Z.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H00NK.faa.1 for reading
sult/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/tmp/
****** Phase 1 of 2, initial predictions ******
****** Step 1/3, current time: 04/23/2025 15:40:06 ******
Create blast database...
[makeblastdb]	Building a new DB, current time: 04/23/2025 15:40:50
[makeblastdb]	New DB name:   /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/tmp/genome-nextpolish_2324984837
[makeblastdb]	New DB title:  /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/quast_corrected_input/genome-nextpolish.fasta
[makeblastdb]	Sequence type: Nucleotide
[makeblastdb]	Keep MBits: T
[makeblastdb]	Maximum file size: 3000000000B
[makeblastdb]	Adding sequences from FASTA; added 187 sequences in 0.0293529 seconds.
[makeblastdb]	1 of 1 task(s) completed at 04/23/2025 15:40:50
Running tblastn, writing output to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/blast_output/tblastn_genome-nextpolish.tsv...
[tblastn]	1 of 1 task(s) completed at 04/23/2025 15:40:52
****** Step 2/3, current time: 04/23/2025 15:40:52 ******
Maximum number of candidate contig per BUSCO limited to: 3
Getting coordinates for candidate regions...
Pre-Augustus scaffold extraction...
Running Augustus prediction using fly as species:
Additional parameters for Augustus are '': 
[augustus]	Please find all logs related to Augustus errors here: /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/augustus.log
[augustus]	1 of 7 task(s) completed at 04/23/2025 15:40:53
[augustus]	3 of 7 task(s) completed at 04/23/2025 15:40:53
[augustus]	4 of 7 task(s) completed at 04/23/2025 15:40:53
[augustus]	5 of 7 task(s) completed at 04/23/2025 15:40:53
[augustus]	6 of 7 task(s) completed at 04/23/2025 15:40:53
[augustus]	7 of 7 task(s) completed at 04/23/2025 15:40:53
Extracting predicted proteins...
****** Step 3/3, current time: 04/23/2025 15:40:53 ******
Running HMMER to confirm orthology of predicted proteins:
Results:
C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:148
0 Complete BUSCOs (C)
0 Complete and single-copy BUSCOs (S)
0 Complete and duplicated BUSCOs (D)
0 Fragmented BUSCOs (F)
148 Missing BUSCOs (M)
148 Total BUSCO groups searched
****** Phase 2 of 2, predictions using species specific training ******
****** Step 1/3, current time: 04/23/2025 15:40:53 ******
Extracting missing and fragmented buscos from the ancestral_variants file...
Running tblastn, writing output to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/blast_output/tblastn_genome-nextpolish_missing_and_frag_rerun.tsv...
[tblastn]	1 of 1 task(s) completed at 04/23/2025 15:40:55
Maximum number of candidate contig per BUSCO limited to: 3
Getting coordinates for candidate regions...
****** Step 2/3, current time: 04/23/2025 15:40:55 ******
Training Augustus using Single-Copy Complete BUSCOs:
Converting predicted genes to short genbank files at 04/23/2025 15:40:55...
All files converted to short genbank files, now running the training scripts at 04/23/2025 15:40:55...
Pre-Augustus scaffold extraction...
Re-running Augustus with the new metaparameters, number of target BUSCOs: 148
[augustus]	1 of 8 task(s) completed at 04/23/2025 15:40:55
[augustus]	2 of 8 task(s) completed at 04/23/2025 15:40:55
[augustus]	4 of 8 task(s) completed at 04/23/2025 15:40:55
[augustus]	5 of 8 task(s) completed at 04/23/2025 15:40:55
[augustus]	6 of 8 task(s) completed at 04/23/2025 15:40:55
[augustus]	7 of 8 task(s) completed at 04/23/2025 15:40:55
[augustus]	8 of 8 task(s) completed at 04/23/2025 15:40:55
Extracting predicted proteins...
****** Step 3/3, current time: 04/23/2025 15:40:55 ******
Running HMMER to confirm orthology of predicted proteins:
[hmmsearch]	1 of 4 task(s) completed at 04/23/2025 15:40:55
[hmmsearch]	3 of 4 task(s) completed at 04/23/2025 15:40:55
[hmmsearch]	4 of 4 task(s) completed at 04/23/2025 15:40:55
Results:
C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:148
0 Complete BUSCOs (C)
0 Complete and single-copy BUSCOs (S)
0 Complete and duplicated BUSCOs (D)
0 Fragmented BUSCOs (F)
148 Missing BUSCOs (M)
148 Total BUSCO groups searched
BUSCO did not find any match. Do not forget to check the file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/augustus.log to exclude a problem regarding Augustus
[bash]	rm: cannot remove ‘/public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/tmp/temp_genome-nextpolish_2324984837’: No such file or directory
BUSCO analysis done with WARNING(s). Total running time: 51.11212730407715 seconds
Results written in /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJDB12113/DRR317926_DRR317949/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/

