Augustus problem?

I'm trying to run the latest version of BUSCO and keep running into what looks like an Augustus error. Any guidance is much appreciated.

Kevin

kevin-mckernans-macbook-pro-3:busco-master kevinmc$ sudo -E python scripts/run_BUSCO.py -i sample_data/target.fa -c 8 -o Test_data_3 -l /Users/kevinmc/busco-master/embryophyta_odb9/ -m geno INFO ****************** Start a BUSCO 3.0.2 analysis, current time: 07/30/2018 18:55:28 ****************** INFO Configuration loaded from /Users/kevinmc/busco-master/config/config.ini INFO Init tools... INFO Check dependencies... INFO Check input file... INFO To reproduce this run: python scripts/run_BUSCO.py -i sample_data/target.fa -o Test_data_3 -l /Users/kevinmc/busco-master/embryophyta_odb9/ -m genome -c 8 -sp arabidopsis INFO Mode is: genome INFO The lineage dataset is: embryophyta_odb9 (eukaryota) INFO Temp directory is ./tmp/ INFO ****** Phase 1 of 2, initial predictions ****** INFO ****** Step 1/3, current time: 07/30/2018 18:55:28 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 07/30/2018 18:55:28 INFO [makeblastdb] New DB name: /Users/kevinmc/busco-master/tmp/Test_data_3_2860704585 INFO [makeblastdb] New DB title: sample_data/target.fa INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 1 sequences in 0.00862789 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 07/30/2018 18:55:28 INFO Running tblastn, writing output to /Users/kevinmc/busco-master/run_Test_data_3/blast_output/tblastn_Test_data_3.tsv... INFO [tblastn] 1 of 1 task(s) completed at 07/30/2018 18:55:32 INFO ****** Step 2/3, current time: 07/30/2018 18:55:32 ****** INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO Pre-Augustus scaffold extraction... INFO Running Augustus prediction using arabidopsis as species: INFO [augustus] Please find all logs related to Augustus errors here: /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/augustus.log INFO [augustus] 2 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 4 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 6 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 8 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 10 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 12 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 14 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 16 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 18 of 19 task(s) completed at 07/30/2018 18:55:32 INFO [augustus] 19 of 19 task(s) completed at 07/30/2018 18:55:32 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 07/30/2018 18:55:32 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO Results: INFO C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1440 INFO 0 Complete BUSCOs (C) INFO 0 Complete and single-copy BUSCOs (S) INFO 0 Complete and duplicated BUSCOs (D) INFO 0 Fragmented BUSCOs (F) INFO 1440 Missing BUSCOs (M) INFO 1440 Total BUSCO groups searched INFO ****** Phase 2 of 2, predictions using species specific training ****** INFO ****** Step 1/3, current time: 07/30/2018 18:55:32 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /Users/kevinmc/busco-master/run_Test_data_3/blast_output/tblastn_Test_data_3_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 07/30/2018 18:56:08 INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO ****** Step 2/3, current time: 07/30/2018 18:56:08 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 07/30/2018 18:56:08... INFO All files converted to short genbank files, now running the training scripts at 07/30/2018 18:56:08... INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 1440 INFO [augustus] 9 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 12 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 15 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 18 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 21 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 24 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 27 of 29 task(s) completed at 07/30/2018 18:56:08 INFO [augustus] 29 of 29 task(s) completed at 07/30/2018 18:56:08 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 07/30/2018 18:56:09 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG093609SU.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360F56.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360QEX.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG0936071Y.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG0936031Y.faa.1 for reading INFO [hmmsearch] 2 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG0936069X.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG093605XN.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360AWY.faa.1 for reading INFO [hmmsearch] 6 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360CWE.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360CFL.faa.1 for reading INFO [hmmsearch] 7 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] 9 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360AX2.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360B4I.faa.1 for reading INFO [hmmsearch] 10 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG093607ZT.faa.1 for reading INFO [hmmsearch] 12 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] 13 of 14 task(s) completed at 07/30/2018 18:56:09 INFO [hmmsearch] Error: Failed to open sequence file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/extracted_proteins/EOG09360A7L.faa.1 for reading INFO [hmmsearch] 14 of 14 task(s) completed at 07/30/2018 18:56:09 INFO Results: INFO C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1440 INFO 0 Complete BUSCOs (C) INFO 0 Complete and single-copy BUSCOs (S) INFO 0 Complete and duplicated BUSCOs (D) INFO 0 Fragmented BUSCOs (F) INFO 1440 Missing BUSCOs (M) INFO 1440 Total BUSCO groups searched WARNING BUSCO did not find any match. Do not forget to check the file /Users/kevinmc/busco-master/run_Test_data_3/augustus_output/augustus.log to exclude a problem regarding Augustus INFO [bash] rm: ./tmp/temp_Test_data_3_2860704585: No such file or directory INFO BUSCO analysis done with WARNING(s). Total running time: 40.9964551926 seconds INFO Results written in /Users/kevinmc/busco-master/run_Test_data_3/