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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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UnboundLocalError: local variable 'AUGUSTUS_BASE' referenced before assignment #850

Open DiegoSafian opened 1 year ago

DiegoSafian commented 1 year ago

Are you using the latest release? yes

Describe the bug The training with Augustus is failing because UnboundLocalError: local variable 'AUGUSTUS_BASE' referenced before assignment

What command did you issue? funannotate predict --species p_turneri_fun \ --input turneri_genome.fasta \ --out turneri_test \ --transcript_evidence /camp/home/safiand/home/users/safiand/Bulk.rna_poeciliidae/turneri/trinity_out_dir/Trinity-GG.fasta \ --rna_bam /camp/home/safiand/home/users/safiand/genome_annotation/turneri/rna_protein_turneri/RNA_alignmentAligned.sortedByCoord.out.bam \ --protein_evidence /camp/home/safiand/home/users/safiand/genome_annotation/protein_pociliidae_ensambl/proteinsfishes.fasta \ --genemark_gtf /camp/home/safiand/home/users/safiand/genome_annotation/turneri/rna_protein_turneri/braker/prote_rna_turneri/GeneMark-ETP/genemark.gtf \ --busco_db actinopterygii \ --organism other \ --max_intronlen 100000 \ --optimize_augustus \ --repeats2evm \ --cpus 32 \ --force \ --AUGUSTUS_CONFIG_PATH=/camp/home/safiand/home/users/safiand/bin/augustus_config_system \ --GENEMARK_PATH=/camp/home/safiand/home/users/safiand/bin/gmes_linux_64_mod

Logfiles Traceback (most recent call last): File "/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 1415, in main lib.trainAugustus(AUGUSTUS_BASE, aug_species, trainingset, UnboundLocalError: local variable 'AUGUSTUS_BASE' referenced before assignment

OS/Install Information

Checking Environmental Variables... $FUNANNOTATE_DB=/camp/home/safiand/home/users/safiand/funannotate_db $PASAHOME=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/config/ ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 proteinortho: 6.1.6 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: pigz not installed ERROR: signalp not installed

DiegoSafian commented 1 year ago

It appears there is a problem with Augustus.

Running funannotate predict unit testing Downloading: https://osf.io/te2pf/download?version=1 Bytes: 1489808 8192 [0.55%]16384 [1.10%]24576 [1.65%]32768 [2.20%]40960 [2.75%]49152 [3.30%]57344 [3.85%]65536 [4.40%]73728 [4.95%]81920 [5.50%]90112 [6.05%]98304 [6.60%]106496 [7.15%]114688 [7.70%]122880 [8.25%]131072 [8.80%]139264 [9.35%]147456 [9.90%]155648 [10.45%]163840 [11.00%]172032 [11.55%]180224 [12.10%]188416 [12.65%]196608 [13.20%]204800 [13.75%]212992 [14.30%]221184 [14.85%]229376 [15.40%]237568 [15.95%]245760 [16.50%]253952 [17.05%]262144 [17.60%]270336 [18.15%]278528 [18.70%]286720 [19.25%]294912 [19.80%]303104 [20.35%]311296 [20.90%]319488 [21.44%]327680 [21.99%]335872 [22.54%]344064 [23.09%]352256 [23.64%]360448 [24.19%]368640 [24.74%]376832 [25.29%]385024 [25.84%]393216 [26.39%]401408 [26.94%]409600 [27.49%]417792 [28.04%]425984 [28.59%]434176 [29.14%]442368 [29.69%]450560 [30.24%]458752 [30.79%]466944 [31.34%]475136 [31.89%]483328 [32.44%]491520 [32.99%]499712 [33.54%]507904 [34.09%]516096 [34.64%]524288 [35.19%]532480 [35.74%]540672 [36.29%]548864 [36.84%]557056 [37.39%]565248 [37.94%]573440 [38.49%]581632 [39.04%]589824 [39.59%]598016 [40.14%]606208 [40.69%]614400 [41.24%]622592 [41.79%]630784 [42.34%]638976 [42.89%]647168 [43.44%]655360 [43.99%]663552 [44.54%]671744 [45.09%]679936 [45.64%]688128 [46.19%]696320 [46.74%]704512 [47.29%]712704 [47.84%]720896 [48.39%]729088 [48.94%]737280 [49.49%]745472 [50.04%]753664 [50.59%]761856 [51.14%]770048 [51.69%]778240 [52.24%]786432 [52.79%]794624 [53.34%]802816 [53.89%]811008 [54.44%]819200 [54.99%]827392 [55.54%]835584 [56.09%]843776 [56.64%]851968 [57.19%]860160 [57.74%]868352 [58.29%]876544 [58.84%]884736 [59.39%]892928 [59.94%]901120 [60.49%]909312 [61.04%]917504 [61.59%]925696 [62.14%]933888 [62.69%]942080 [63.23%]950272 [63.78%]958464 [64.33%]966656 [64.88%]974848 [65.43%]983040 [65.98%]991232 [66.53%]999424 [67.08%]1007616 [67.63%]1015808 [68.18%]1024000 [68.73%]1032192 [69.28%]1040384 [69.83%]1048576 [70.38%]1056768 [70.93%]1064960 [71.48%]1073152 [72.03%]1081344 [72.58%]1089536 [73.13%]1097728 [73.68%]1105920 [74.23%]1114112 [74.78%]1122304 [75.33%]1130496 [75.88%]1138688 [76.43%]1146880 [76.98%]1155072 [77.53%]1163264 [78.08%]1171456 [78.63%]1179648 [79.18%]1187840 [79.73%]1196032 [80.28%]1204224 [80.83%]1212416 [81.38%]1220608 [81.93%]1228800 [82.48%]1236992 [83.03%]1245184 [83.58%]1253376 [84.13%]1261568 [84.68%]1269760 [85.23%]1277952 [85.78%]1286144 [86.33%]1294336 [86.88%]1302528 [87.43%]1310720 [87.98%]1318912 [88.53%]1327104 [89.08%]1335296 [89.63%]1343488 [90.18%]1351680 [90.73%]1359872 [91.28%]1368064 [91.83%]1376256 [92.38%]1384448 [92.93%]1392640 [93.48%]1400832 [94.03%]1409024 [94.58%]1417216 [95.13%]1425408 [95.68%]1433600 [96.23%]1441792 [96.78%]1449984 [97.33%]1458176 [97.88%]1466368 [98.43%]1474560 [98.98%]1482752 [99.53%]1489808 [100.00%]------------------------------------------------------- [Dec 31 09:33 AM]: OS: CentOS Linux 7, 32 cores, ~ 263 GB RAM. Python: 3.8.15 [Dec 31 09:33 AM]: Running funannotate v1.8.13 [Dec 31 09:33 AM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction. [Dec 31 09:33 AM]: Skipping CodingQuarry as no --rna_bam passed [Dec 31 09:33 AM]: Parsed training data, run ab-initio gene predictors as follows: Program Training-Method augustus pretrained
glimmerhmm busco
snap busco
[Dec 31 09:33 AM]: Loading genome assembly and parsing soft-masked repetitive sequences [Dec 31 09:33 AM]: Genome loaded: 6 scaffolds; 3,776,588 bp; 19.75% repeats masked [Dec 31 09:33 AM]: Mapping 1,065 proteins to genome using diamond and exonerate [Dec 31 09:33 AM]: Found 1,505 preliminary alignments with diamond in 0:00:01 --> generated FASTA files for exonerate in 0:00:00 Progress: 0.00% Progress: 10.63% Progress: 30.70% Progress: 49.50% Progress: 67.51% Progress: 85.25% Progress: 99.87% Progress: 99.93% Progress: 99.93% Progress: 99.93% Progress: 99.93% Progress: 99.93% [Dec 31 09:34 AM]: Exonerate finished in 0:00:12: found 1,270 alignments [Dec 31 09:34 AM]: Running BUSCO to find conserved gene models for training ab-initio predictors [Dec 31 09:37 AM]: 370 valid BUSCO predictions found, validating protein sequences [Dec 31 09:38 AM]: 367 BUSCO predictions validated [Dec 31 09:38 AM]: Running Augustus gene prediction using saccharomyces parameters Progress: 0.00% [Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=1 --predictionEnd=312565.38639533357 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022975.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022974.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=1 --predictionEnd=278016.7473349764 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022970.1.fa [Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022971.1.fa [Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=267676.1293727999 --predictionEnd=545352.2587455998 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022973.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=693683.5714535144 --predictionEnd=1050525.3571802715 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022972.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=346841.7857267572 --predictionEnd=703683.5714535144 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022972.1.fa [Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=1 --predictionEnd=356841.7857267572 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022972.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=302565.38639533357 --predictionEnd=615130.7727906671 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022975.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=268016.7473349764 --predictionEnd=546033.4946699528 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022970.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

[Dec 31 09:38 AM]: CMD ERROR: augustus --species=saccharomyces --predictionStart=1 --predictionEnd=277676.1293727999 --extrinsicCfgFile=/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/config/extrinsic.E.XNT.RM.cfg --hintsfile=annotate/predict_misc/hints.ALL.gff --AUGUSTUS_CONFIG_PATH=annotate/predict_misc/ab_initio_parameters/augustus --softmasking=1 --gff3=on --UTR=off --stopCodonExcludedFromCDS=False augustus_tmp_e6e201c6-f588-4e19-9593-b2c560ba8f1e/CP022973.1.fa [Dec 31 09:38 AM]: augustus: ERROR Could not locate command line parameters file: annotate/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

nextgenusfs commented 1 year ago

I think its because this version of funannotate is not compatible with Augustus v3.5. You can either try to install the latest from the master branch via pip or downgrade Augustus.

DiegoSafian commented 1 year ago

Hi Joe,

Thanks for your reply. I followed your advice and updated using python -m pip install git+https://github.com/nextgenusfs/funannotate.git alone and then with a downgraded augustus to 3.4 (3.3.3 did not work). However, I got the same error. It appears to me that Augustus is running well till some points and then dies. Could you please, take a look at the report text and busco.log?

text report

start Mon Jan 9 10:16:04 GMT 2023
/camp/apps/eb/software/Anaconda3/2020.07/condabin/conda
rm: cannot remove ‘/camp/home/safiand/home/users/safiand/genome_annotation/turneri/funannotate/turneri’: No such file or directory
-------------------------------------------------------
[Jan 09 10:16 AM]: OS: CentOS Linux 7, 32 cores, ~ 263 GB RAM. Python: 3.8.15
[Jan 09 10:16 AM]: Running funannotate v1.8.14
[Jan 09 10:16 AM]: Skipping CodingQuarry as --organism=other. Pass a weight larger than 0 to run CQ, ie --weights codingquarry:1
[Jan 09 10:16 AM]: Parsed training data, run ab-initio gene predictors as follows:
  Program      Training-Method
  augustus     busco          
  genemark     selftraining   
  glimmerhmm   busco          
  snap         busco          
[Jan 09 10:19 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Jan 09 10:19 AM]: Genome loaded: 1,136 scaffolds; 598,381,391 bp; 25.63% repeats masked
[Jan 09 10:19 AM]: Aligning transcript evidence to genome with minimap2
[Jan 09 10:20 AM]: Found 149,570 alignments, wrote GFF3 and Augustus hints to file
[Jan 09 10:20 AM]: Extracting hints from RNA-seq BAM file using bam2hints
[Jan 09 10:26 AM]: Mapping 227,942 proteins to genome using diamond and exonerate
[Jan 09 10:49 AM]: Found 487,379 preliminary alignments with diamond in 0:16:48 --> generated FASTA files for exonerate in 0:06:21
[Jan 09 11:51 AM]: Exonerate finished in 1:01:31: found 48,478 alignments
     Progress: 1713 complete, 0 failed, 485666 remaining        
     Progress: 2194 complete, 0 failed, 485185 remaining        
     Progress: 2569 complete, 0 failed, 484810 remaining        
     Progress: 2846 complete, 0 failed, 484533 remaining        
     Progress: 3112 complete, 0 failed, 484267 remaining        
   ................. and so on .....
     Progress: 486814 complete, 0 failed, 565 remaining        
     Progress: 487013 complete, 0 failed, 366 remaining        
     Progress: 487198 complete, 0 failed, 181 remaining        
     Progress: 487379 complete, 0 failed, 0 remaining        
[Jan 09 11:53 AM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Jan 09 03:10 PM]: 4,248 valid BUSCO predictions found, validating protein sequences
[Jan 09 03:27 PM]: 4,237 BUSCO predictions validated
[Jan 09 03:27 PM]: Training Augustus using BUSCO gene models
Traceback (most recent call last):
  File "/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/bin/funannotate", line 8, in <module>
    sys.exit(main())
  File "/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main
    mod.main(arguments)

  File "/camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 1418, in main
    lib.trainAugustus(AUGUSTUS_BASE, aug_species, trainingset,
UnboundLocalError: local variable 'AUGUSTUS_BASE' referenced before assignment
finish Mon Jan 9 15:27:21 GMT 2023

busco.log

INFO    ****************** Start a BUSCO 2.0 analysis, current time: 01/09/2023 11:53:01 ******************
INFO    The lineage dataset is: actinopterygii_odb9 (eukaryota)
INFO    Mode is: genome
INFO    Maximum number of regions limited to: 3
INFO    To reproduce this run: python /camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py -i /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/genome.softmasked.fa -o turneri_fun -l /camp/home/safiand/home/users/safiand/funannotate_db/actinopterygii/ -m genome -c 32 -sp zebrafish
INFO    Check dependencies...
INFO    Check input file...
INFO    Temp directory is ./tmp/

INFO    ****** Phase 1 of 2, initial predictions ******
INFO    ****** Step 1/3, current time: 01/09/2023 11:53:04 ******
INFO    Create blast database...
INFO    [makeblastdb]   Building a new DB, current time: 01/09/2023 11:53:04
INFO    [makeblastdb]   New DB name:   /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco/tmp/turneri_fun_533128093
INFO    [makeblastdb]   New DB title:  /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/genome.softmasked.fa
INFO    [makeblastdb]   Sequence type: Nucleotide
INFO    [makeblastdb]   Keep Linkouts: T
INFO    [makeblastdb]   Keep MBits: T
INFO    [makeblastdb]   Maximum file size: 1000000000B
INFO    [makeblastdb]   Adding sequences from FASTA; added 1136 sequences in 4.75432 seconds.
INFO    Running tblastn, writing output to /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco/run_turneri_fun/blast_output/tblastn_turneri_fun.tsv...
INFO    ****** Step 2/3, current time: 01/09/2023 12:11:48 ******
INFO    Getting coordinates for candidate regions...
INFO    Pre-Augustus scaffold extraction...
INFO    Running Augustus prediction using zebrafish as species:
INFO    [augustus] Please find all logs related to Augustus here: /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco/run_turneri_fun/augustus_output/augustus.log
INFO    01/09/2023 12:12:04 =>  0% of predictions performed (6839 to be done)
INFO    01/09/2023 12:46:21 =>  10% of predictions performed (684/6839 candidate regions)
INFO    01/09/2023 13:03:36 =>  20% of predictions performed (1368/6839 candidate regions)
INFO    01/09/2023 13:15:43 =>  30% of predictions performed (2052/6839 candidate regions)
INFO    01/09/2023 13:25:29 =>  40% of predictions performed (2737/6839 candidate regions)
INFO    01/09/2023 13:33:58 =>  50% of predictions performed (3420/6839 candidate regions)
INFO    01/09/2023 13:42:24 =>  60% of predictions performed (4109/6839 candidate regions)
INFO    01/09/2023 13:50:11 =>  70% of predictions performed (4793/6839 candidate regions)
INFO    01/09/2023 13:58:19 =>  80% of predictions performed (5473/6839 candidate regions)
INFO    01/09/2023 14:07:44 =>  90% of predictions performed (6156/6839 candidate regions)
INFO    01/09/2023 14:17:28 =>  100% of predictions performed
INFO    Extracting predicted proteins...
INFO    ****** Step 3/3, current time: 01/09/2023 14:22:17 ******
INFO    Running HMMER to confirm orthology of predicted proteins:
INFO    01/09/2023 14:22:17 =>  0% of predictions performed (6838 to be done)
INFO    01/09/2023 14:22:38 =>  10% of predictions performed (685/6838 candidate proteins)
INFO    01/09/2023 14:23:30 =>  20% of predictions performed (1368/6838 candidate proteins)
INFO    01/09/2023 14:24:58 =>  30% of predictions performed (2052/6838 candidate proteins)
INFO    01/09/2023 14:27:00 =>  40% of predictions performed (2737/6838 candidate proteins)
INFO    01/09/2023 14:29:36 =>  50% of predictions performed (3420/6838 candidate proteins)
INFO    01/09/2023 14:32:32 =>  60% of predictions performed (4106/6838 candidate proteins)
INFO    01/09/2023 14:36:08 =>  70% of predictions performed (4795/6838 candidate proteins)
INFO    01/09/2023 14:39:33 =>  80% of predictions performed (5476/6838 candidate proteins)
INFO    01/09/2023 14:43:26 =>  90% of predictions performed (6190/6838 candidate proteins)
INFO    01/09/2023 14:47:09 =>  100% of predictions performed
INFO    Results:
INFO    C:94.5%[S:92.7%,D:1.8%],F:3.6%,M:1.9%,n:4584
INFO    4331 Complete BUSCOs (C)
INFO    4248 Complete and single-copy BUSCOs (S)
INFO    83 Complete and duplicated BUSCOs (D)
INFO    167 Fragmented BUSCOs (F)
INFO    86 Missing BUSCOs (M)
INFO    4584 Total BUSCO groups searched

INFO    ****** Phase 2 of 2, predictions using species specific training ******
INFO    ****** Step 1/3, current time: 01/09/2023 14:47:17 ******
INFO    Extracting missing and fragmented buscos from the ancestral_variants file...
INFO    Running tblastn, writing output to /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco/run_turneri_fun/blast_output/tblastn_turneri_fun_missing_and_frag_rerun.tsv...
INFO    Getting coordinates for candidate regions...
INFO    ****** Step 2/3, current time: 01/09/2023 14:58:39 ******
INFO    Training Augustus using Single-Copy Complete BUSCOs:
INFO    01/09/2023 14:58:39 =>  Converting predicted genes to short genbank files...
INFO    01/09/2023 15:08:10 =>  All files converted to short genbank files, now running the training scripts...
INFO    Pre-Augustus scaffold extraction...
INFO    Re-running Augustus with the new metaparameters, number of target BUSCOs: 253
INFO    01/09/2023 15:09:19 =>  0% of predictions performed (447 to be done)
INFO    01/09/2023 15:09:19 =>  10% of predictions performed (48/447 candidate regions)
INFO    01/09/2023 15:09:20 =>  20% of predictions performed (90/447 candidate regions)
INFO    01/09/2023 15:09:21 =>  30% of predictions performed (143/447 candidate regions)
INFO    01/09/2023 15:09:22 =>  40% of predictions performed (183/447 candidate regions)
INFO    01/09/2023 15:09:23 =>  50% of predictions performed (224/447 candidate regions)
INFO    01/09/2023 15:09:26 =>  60% of predictions performed (280/447 candidate regions)
INFO    01/09/2023 15:09:27 =>  70% of predictions performed (314/447 candidate regions)
INFO    01/09/2023 15:09:29 =>  80% of predictions performed (374/447 candidate regions)
INFO    01/09/2023 15:09:30 =>  100% of predictions performed
INFO    Extracting predicted proteins...
INFO    ****** Step 3/3, current time: 01/09/2023 15:09:36 ******
INFO    Running HMMER to confirm orthology of predicted proteins:
INFO    01/09/2023 15:09:36 =>  0% of predictions performed (0 to be done)
INFO    01/09/2023 15:09:36 =>  100% of predictions performed
INFO    Results:
INFO    C:94.5%[S:92.7%,D:1.8%],F:3.6%,M:1.9%,n:4584
INFO    4331 Complete BUSCOs (C)
INFO    4248 Complete and single-copy BUSCOs (S)
INFO    83 Complete and duplicated BUSCOs (D)
INFO    167 Fragmented BUSCOs (F)
INFO    86 Missing BUSCOs (M)
INFO    4584 Total BUSCO groups searched

INFO    BUSCO analysis done. Total running time: 11847.195273399353 seconds
INFO    Results written in /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco/run_turneri_fun/

INFO    ****************** Start a BUSCO 2.0 analysis, current time: 01/09/2023 15:14:36 ******************
INFO    The lineage dataset is: actinopterygii_odb9 (eukaryota)
INFO    Mode is: proteins
INFO    To reproduce this run: python /camp/home/safiand/home/users/safiand/.conda/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py -i /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco_augustus.proteins.fasta -o turneri_fun -l /camp/home/safiand/home/users/safiand/funannotate_db/actinopterygii/ -m proteins -c 64 -sp zebrafish
INFO    Check dependencies...
INFO    Check input file...
INFO    Temp directory is ./tmp/
INFO    Running HMMER on the proteins:
INFO    01/09/2023 15:14:36 =>  0% of predictions performed (4584 to be done)
INFO    01/09/2023 15:14:53 =>  10% of predictions performed (461/4584 candidate proteins)
INFO    01/09/2023 15:15:17 =>  20% of predictions performed (922/4584 candidate proteins)
INFO    01/09/2023 15:15:56 =>  30% of predictions performed (1376/4584 candidate proteins)
INFO    01/09/2023 15:16:52 =>  40% of predictions performed (1834/4584 candidate proteins)
INFO    01/09/2023 15:18:02 =>  50% of predictions performed (2293/4584 candidate proteins)
INFO    01/09/2023 15:19:30 =>  60% of predictions performed (2752/4584 candidate proteins)
INFO    01/09/2023 15:21:10 =>  70% of predictions performed (3209/4584 candidate proteins)
INFO    01/09/2023 15:23:05 =>  80% of predictions performed (3672/4584 candidate proteins)
INFO    01/09/2023 15:24:58 =>  90% of predictions performed (4131/4584 candidate proteins)
INFO    01/09/2023 15:26:39 =>  100% of predictions performed
INFO    Results:
INFO    C:92.5%[S:92.4%,D:0.1%],F:0.1%,M:7.4%,n:4584
INFO    4240 Complete BUSCOs (C)
INFO    4237 Complete and single-copy BUSCOs (S)
INFO    3 Complete and duplicated BUSCOs (D)
INFO    5 Fragmented BUSCOs (F)
INFO    339 Missing BUSCOs (M)
INFO    4584 Total BUSCO groups searched

INFO    BUSCO analysis done. Total running time: 748.6362130641937 seconds
INFO    Results written in /camp/lab/cardoso-moreiam/home/users/safiand/genome_annotation/turneri/funannotate/turneri/predict_misc/busco_proteins/run_turneri_fun/

I perhaps should try reinstalling the conda env and then downgrade augustus without the -m pip install git+https://github.com/nextgenusfs/funannotate.git ?

max-hence commented 1 year ago

Hi Joe, I have got the same problem with Augustus. I'm working on conda env on Linux and either the funannotate predict run never stops either I don't manage to link augustus to Funnanotate. Could you please show me the good version of augustus compatible with funannotate and how to set the environnement ?

Thank you for your help Max

DiegoSafian commented 1 year ago

Hi., The problem finally is solved. I just re-installed funnanotate using conda install funannotate insted ofconda install -c bioconda funannotate and that make it. Not idea how.

hafizmtalha commented 1 year ago

installed funannotate today and still facing the same problem.

Hi., The problem finally is solved. I just re-installed funnanotate using conda install funannotate insted ofconda install -c bioconda funannotate and that make it. Not idea how.

SLAment commented 1 year ago

I seem to have the same issue with Augustus 3.3.3 and Funannotate 1.8.13 :/

nextgenusfs commented 1 year ago

I think the latest v1.8.15 should be available on conda as of this morning. It is pinned to augustus v3.5.0, hopefully that solves the frustrating augustus install issues.....