not running,but no error report

[YDD99]

(funannotate) wangyuanbing@wangyb-System:~/Desktop/CZY/funannotate$ funannotate predict -i '/home/wangyuanbing/Desktop/CZY/funannotate/scaffolds_clean_sort_mask.fasta' --species "Hypocrella raciborskii" -o funannotate --cpus 4

[Nov 14 05:10 PM]: OS: Linux Mint 20.3, 8 cores, ~ 33 GB RAM. Python: 3.7.12 [Nov 14 05:10 PM]: Running funannotate v1.8.13

^CTraceback (most recent call last): File "/home/wangyuanbing/miniconda3/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/predict.py", line 253, in main if lib.which('bam2hints'): File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/library.py", line 853, in which stderr=devnull, universal_newlines=True).communicate() File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/subprocess.py", line 956, in communicate self.wait() File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/subprocess.py", line 1019, in wait return self._wait(timeout=timeout) File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/subprocess.py", line 1653, in _wait (pid, sts) = self._try_wait(0) File "/home/wangyuanbing/miniconda3/envs/funannotate/lib/python3.7/subprocess.py", line 1611, in _try_wait (pid, sts) = os.waitpid(self.pid, wait_flags) KeyboardInterrupt (funannotate) wangyuanbing@wangyb-System:~/Desktop/CZY/funannotate$ ^C

[hyphaltip]

it is hard to help here without more info or an example of data that replicates the problem. does the funannotate test work at all for you (i know on current version it seems slow) did you run funannotate check --show-versions to see that all dependency software is installed properly.

[YDD99]

(funannotate) wangyuanbing@wangyb-System:~$ funannotate check --show-versions

Checking dependencies for 1.8.13

You are running Python v 3.7.12. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.5.3 natsort: 8.2.0 numpy: 1.21.6 pandas: 1.3.5 psutil: 5.9.2 requests: 2.28.1 scikit-learn: 1.0.2 scipy: 1.7.3 seaborn: 0.12.0 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: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.52 Hash::Merge: 0.302 JSON: 4.10 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 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/home/wangyuanbing/funannotate_db $PASAHOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/wangyuanbing/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/wangyuanbing/miniconda3/envs/funannotate/bin:/home/wangyuanbing/miniconda3/bin:/home/wangyuanbing/miniconda3/condabin:/home/wangyuanbing/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin All 6 environmental variables are set

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 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.69_lic 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 pigz: pigz 2.6 proteinortho: 6.1.1 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) 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: 0.36 All 37 external dependencies are installed

as you see,i did funannotate check --show-versions, looks like no problem also i did funannotate test before ,spent almost two days and no results,i will try it again from begining, thank you

[nextgenusfs]

Funannotate v1.8.13 and below is not compatible with Augustus v3.4 and above. That's why it doesn't finish. So downgrade Augustus or upgrade funannotate to latest in master.

[YDD99]

thank you very much ,thank you!