[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H00SC.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H01AW.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H01B8.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H00EY.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H02HW.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H016C.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H001O.faa.1 for reading
[hmmsearch]	Error: Failed to open sequence file /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/extracted_proteins/POG091H01RS.faa.1 for reading
ed/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/blast_output/tblastn_genome-nextpolish.tsv...
[tblastn]	1 of 1 task(s) completed at 06/09/2025 00:17:12
****** Step 2/3, current time: 06/09/2025 00:17:12 ******
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/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/augustus_output/augustus.log
[augustus]	2 of 15 task(s) completed at 06/09/2025 00:17:12
[augustus]	5 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	6 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	8 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	9 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	11 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	12 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	14 of 15 task(s) completed at 06/09/2025 00:17:13
[augustus]	15 of 15 task(s) completed at 06/09/2025 00:17:13
Extracting predicted proteins...
****** Step 3/3, current time: 06/09/2025 00:17:13 ******
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: 06/09/2025 00:17:13 ******
Extracting missing and fragmented buscos from the ancestral_variants file...
Running tblastn, writing output to /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.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 06/09/2025 00:17:28
Maximum number of candidate contig per BUSCO limited to: 3
Getting coordinates for candidate regions...
****** Step 2/3, current time: 06/09/2025 00:17:28 ******
Training Augustus using Single-Copy Complete BUSCOs:
Converting predicted genes to short genbank files at 06/09/2025 00:17:28...
All files converted to short genbank files, now running the training scripts at 06/09/2025 00:17:28...
Pre-Augustus scaffold extraction...
Re-running Augustus with the new metaparameters, number of target BUSCOs: 148
[augustus]	2 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	4 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	7 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	9 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	11 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	12 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	14 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	16 of 17 task(s) completed at 06/09/2025 00:17:29
[augustus]	17 of 17 task(s) completed at 06/09/2025 00:17:29
Extracting predicted proteins...
****** Step 3/3, current time: 06/09/2025 00:17:29 ******
Running HMMER to confirm orthology of predicted proteins:
[hmmsearch]	1 of 8 task(s) completed at 06/09/2025 00:17:29
[hmmsearch]	4 of 8 task(s) completed at 06/09/2025 00:17:29
[hmmsearch]	5 of 8 task(s) completed at 06/09/2025 00:17:29
[hmmsearch]	6 of 8 task(s) completed at 06/09/2025 00:17:29
[hmmsearch]	7 of 8 task(s) completed at 06/09/2025 00:17:29
[hmmsearch]	8 of 8 task(s) completed at 06/09/2025 00:17:29
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/PRJEB67829/ERR12157767/2.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/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/tmp/temp_genome-nextpolish_1102778941’: No such file or directory
BUSCO analysis done with WARNING(s). Total running time: 33.25218892097473 seconds
Results written in /public/home/zhaichaoyu/project/LR-seq/metaproject/result/PRJEB67829/ERR12157767/2.Analysis/Assemblybased/2.Polish/metaquast_out/busco_stats/run_genome-nextpolish/

