hyphaltip
commented
2 years ago did you just try and lower number of required training models with --min_training_models 190 given to predict -> (default is 200).
Open Niohuruzh opened 2 years ago
hyphaltip
commented
2 years ago did you just try and lower number of required training models with --min_training_models 190 given to predict -> (default is 200).
hyphaltip
commented
2 years ago This is a little disturbing though
[Jul 14 09:37 PM]: Found 241,445 preliminary alignments --> aligning with exonerate
[Jul 14 09:46 PM]: Exonerate finished: found 1,378 alignments
[Jul 14 09:46 PM]: Filtering PASA data for suitable training set
[Jul 14 09:47 PM]: 198 of 6,193 models pass training parametersAre you sure your species is close to Cryptococcus that this is working well? What is your overall BUSCO score for this genome - if it is low that might not bode well for general gene prediction you are going to be doing. or does this reflect RNAseq that isn't matching well for finding ORFs?
hyphaltip
commented
1 year ago You can set the min training number lower with the --min_training_models models parameter.
On Thu, Jul 14, 2022 at 6:48 AM Niohuruzh @.***> wrote:
Hi
Are you using the latest release? Funannotate v1.8.7
Describe the bug [07/14/22 13:04:50]: 4 models fail blast identity threshold [07/14/22 13:04:51]: 5,992 models will be ignored for training Augustus [07/14/22 13:04:52]: 199 of 6,193 models pass training parameters [07/14/22 13:04:52]: Not enough gene models 199 to train Augustus (200 required), exiting
What command did you issue? funannotate predict -i W3767_clean_sort_mask.fasta --strain W3767 --species W3767 --isolate W3767 -o fun --genemark_gtf genemark.gtf --busco_seed_species cryptococcus_neoformans_gattii --busco_db dikarya --cpus 40 --repeats2evm --no-evm-partitions
Logfiles Please provide relavent log files of the error.
OS/Install Information
funannotate check --show-versions
Checking dependencies for 1.8.7
You are running Python v 3.7.12. Now checking python packages... biopython: 1.77 goatools: 1.2.3 matplotlib: 3.5.2 natsort: 8.1.0 numpy: 1.21.6 pandas: 1.3.5 psutil: 5.9.1 requests: 2.28.1 scikit-learn: 1.0.2 scipy: 1.7.3 seaborn: 0.11.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.70 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.858 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.27 Getopt::Long: 2.52 Hash::Merge: 0.302 JSON: 4.07 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 threads: 2.25 threads::shared: 1.61 ERROR: Bio::Perl not installed, install with cpanm Bio::Perl
Checking Environmental Variables... $FUNANNOTATE_DB=/home/leigod/funannotate_db $PASAHOME=/home/leigod/anaconda3/envs/funannotate/opt/pasa-2.4.1 $TRINITYHOME=/home/leigod/anaconda3/envs/funannotate/opt/trinity-2.8.5/ $EVM_HOME=/home/leigod/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config $GENEMARK_PATH=/home/leigod/software/gmes_linux_64_4 All 6 environmental variables are set
Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.8 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15gmes_petap.pl: 4.69_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.15-internal kallisto: 0.46.1 mafft: v7.505 (2022/Apr/10) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 proteinortho: 6.1.0 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.15 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 39 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: signalp not installed
Is there troubleshooting for this Looking forward your reply
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Jason Stajich - @.***
Hi
Are you using the latest release? Funannotate v1.8.7
Describe the bug
What command did you issue?
funannotate predict -i W3767_clean_sort_mask.fasta --strain W3767 --species W3767 --isolate W3767 -o fun --genemark_gtf genemark.gtf --busco_seed_species cryptococcus_neoformans_gattii --busco_db dikarya --cpus 40 --repeats2evm --no-evm-partitionsLogfiles Please provide relavent log files of the error.
OS/Install Information
Is there troubleshooting for this Looking forward your reply