Funannotate compare stuck at the Proteinortho step for 2 days. The command is at sleep.

[akshayoo]

funannotate compare -i Cross_sp_Compare_GBK/*.gbk -o Cross_compare_results --cpus 24

[Oct 22 10:15 AM]: OS: Ubuntu 20.04, 24 cores, ~ 231 GB RAM. Python: 3.8.19 [Oct 22 10:15 AM]: Running 1.8.17 [Oct 22 10:15 AM]: Now parsing 11 genomes [Oct 22 10:15 AM]: working on Fusarium boothii [Oct 22 10:16 AM]: working on Fusarium equiseti [Oct 22 10:16 AM]: working on Fusarium hainanense [Oct 22 10:16 AM]: working on Fusarium humuli [Oct 22 10:17 AM]: working on Fusarium irregulare [Oct 22 10:17 AM]: working on Fusarium kyushuense [Oct 22 10:17 AM]: working on Fusarium langsethiae [Oct 22 10:17 AM]: working on Fusarium luffae [Oct 22 10:18 AM]: working on Fusarium pseudograminearum [Oct 22 10:18 AM]: working on Fusarium equiseti SF5 [Oct 22 10:18 AM]: working on Fusarium vanenatum [Oct 22 10:19 AM]: No secondary metabolite annotations found [Oct 22 10:19 AM]: Summarizing PFAM domain results /home/user/.local/lib/python3.8/site-packages/sklearn/manifold/_mds.py:298: FutureWarning: The default value of normalized_stress will change to 'auto' in version 1.4. To suppress this warning, manually set the value of normalized_stress. warnings.warn( [Oct 22 10:19 AM]: Summarizing InterProScan results [Oct 22 10:19 AM]: Loading InterPro descriptions /home/user/.local/lib/python3.8/site-packages/sklearn/manifold/_mds.py:298: FutureWarning: The default value of normalized_stress will change to 'auto' in version 1.4. To suppress this warning, manually set the value of normalized_stress. warnings.warn( [Oct 22 10:19 AM]: Summarizing MEROPS protease results [Oct 22 10:19 AM]: found 13/102 MEROPS familes with stdev >= 1.000000 [Oct 22 10:19 AM]: Summarizing CAZyme results [Oct 22 10:19 AM]: found 24/157 CAZy familes with stdev >= 1.000000 [Oct 22 10:19 AM]: Summarizing COG results [Oct 22 10:19 AM]: No SignalP annotations found [Oct 22 10:19 AM]: Summarizing fungal transcription factors [Oct 22 10:19 AM]: Running GO enrichment for each genome WARNING: skipping Fusarium_vanenatum.txt as no GO terms WARNING: skipping Fusarium_irregulare.txt as no GO terms WARNING: skipping Fusarium_humuli.txt as no GO terms WARNING: skipping Fusarium_hainanense.txt as no GO terms WARNING: skipping Fusarium_equiseti.txt as no GO terms WARNING: skipping Fusarium_pseudograminearum.txt as no GO terms WARNING: skipping Fusarium_boothii.txt as no GO terms WARNING: skipping Fusarium_kyushuense.txt as no GO terms WARNING: skipping Fusarium_luffae.txt as no GO terms WARNING: skipping Fusarium_langsethiae.txt as no GO terms [Oct 22 10:19 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...

[akshayoo]

funannotate check --show-versions

Checking dependencies for 1.8.17

You are running Python v 3.8.19. Now checking python packages... biopython: 1.79 goatools: 1.4.12 matplotlib: 3.7.5 natsort: 8.4.0 numpy: 1.24.4 pandas: 2.0.3 psutil: 6.0.0 requests: 2.32.3 scikit-learn: 1.3.2 scipy: 1.10.1 seaborn: 0.13.2 All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.858 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.58 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.03 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: 5.17 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/user/funannotate_db/ $PASAHOME=/home/user/anaconda3/envs/funannotate/opt/pasa-2.5.3 $TRINITYHOME=/home/user/anaconda3/envs/funannotate/opt/trinity-2.1.1 $EVM_HOME=/home/user/anaconda3/envs/funannotate/opt/evidencemodeler-2.1.0 $AUGUSTUS_CONFIG_PATH=/home/user/anaconda3/envs/augustus/config/ ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies... PASA: 2.5.3 CodingQuarry: 2.0 Trinity: 2.15.2 augustus: 3.5.0 bamtools: bamtools 2.5.2 bedtools: bedtools v2.31.1 blat: BLAT v39x1 diamond: 2.1.8 emapper.py: 2.1.12-3-g3666cb0 ete3: 3.1.3 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2024-10-10 hisat2: 2.2.1 hmmscan: HMMER 3.4 (Aug 2023) hmmsearch: HMMER 3.4 (Aug 2023) java: 22.0.1-internal kallisto: 0.46.1 mafft: v7.526 (2024/Apr/26) makeblastdb: makeblastdb 2.16.0+ minimap2: 2.28-r1209 pigz: 2.8 proteinortho: 6.3.2 pslCDnaFilter: no way to determine salmon: salmon 1.10.3 samtools: samtools 1.21 snap: 2006-07-28 stringtie: 2.2.3 tRNAscan-SE: 2.0.12 (Nov 2022) tantan: tantan 50 tbl2asn: 25.8 tblastn: tblastn 2.16.0+ trimal: trimAl v1.5.rev0 build[2024-05-27] trimmomatic: 0.39 ERROR: gmes_petap.pl not installed ERROR: signalp not installed