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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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genemark probuild takes too long #1048

Open sqwwww opened 2 weeks ago

sqwwww commented 2 weeks ago

hi， I am working on the annotation of a eukaryotic animal with a genome size of approximately 600M and around 280 scaffolds. The program stopped running at the probuild section and hasn't produced any new output for two weeks. Should I stop it now and rerun it, or just wait until it finishes? here is my script:

funannotate predict -i MyAssembly.fa -o fun \
    --species "Mb" \
    --cpus 30 \
    --max_intronlen 5000000 --busco_db actinopterygii --organism other --protein_evidence combined_v2.filt.pep

and here is my gmes.log， the program hasn't produce any new output from 5.26 to 6.12（today）.

/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:41:53 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genome.softmasked.fa  --mask_soft 2000 --mask_margin 0 --low2gff data/in_mask.gff 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:41:54 2024] cat  in_mask.gff   >> plus.gff
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:42:09 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild  --seq data/dna.fna  --allow_x  --stat info/dna.general  --details
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:42:26 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild  --seq data/dna.fna  --allow_x  --stat_fasta info/dna.multi_fasta
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:42:33 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild  --seq data/dna.fna  --allow_x  --substring_n_distr info/dna.gap_distr
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:42:46 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gc_distr.pl --in data/dna.fna  --out info/dna.gc.csv  --w 1000,8000
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:06 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild  --seq /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/data/dna.fna  --split dna.fa  --max_contig 5000000 --min_contig 50000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n  --trace ../../info/training.trace 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:24 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/rescale_gff.pl  --in data/plus.gff  --trace info/training.trace  --out data/plus_training.gff
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:39 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild --seq data/training.fna --stat info/training.general --allow_x  --GC_PRECISION 0  --details
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:40 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/build_mod.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg  --section ES_ini --def /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/heu_dir/heu_05_gcode_1_gc_42.mod 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:40 2024] ln -sf  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_ini/es_ini.mod  run/ini.mod
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:54 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/verify_evidence_gmhmm.pl --in /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/data/plus_training.gff  --out /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_1/plus_hmm.gff  --mod /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_ini/es_ini.mod 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Mon May 20 09:43:54 2024] 338 contigs in list
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:35:59 2024] ln -sf /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_ini/es_ini.mod  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_1/prev.mod
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:05 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/parse_set.pl --section ES_A --cfg  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg  --v 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:06 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section start_ATG   --format INI
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:06 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TAA    --format TERM_TAA
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:06 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TAG    --format TERM_TAG
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:07 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TGA    --format TERM_TGA
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:07 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section donor_GT    --format DONOR 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:07 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section acceptor_AG --format ACCEPTOR 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:16 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:17 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/build_mod.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section ES_A --def prev.mod  --out ES_A_1.mod 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:33 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/verify_evidence_gmhmm.pl --in /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/data/plus_training.gff  --out /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_2/plus_hmm.gff  --mod /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_1/ES_A_1.mod 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Wed May 22 09:36:33 2024] 338 contigs in list
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:26:59 2024] ln -sf /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_1/ES_A_1.mod  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_2/prev.mod
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:03 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/parse_set.pl --section ES_A --cfg  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg  --v 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:03 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section start_ATG   --format INI
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:03 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TAA    --format TERM_TAA
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:04 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TAG    --format TERM_TAG
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:04 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TGA    --format TERM_TGA
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:04 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section donor_GT    --format DONOR 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:05 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section acceptor_AG --format ACCEPTOR 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:18 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:18 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/build_mod.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section ES_A --def prev.mod  --out ES_A_2.mod 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:34 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/verify_evidence_gmhmm.pl --in /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/data/plus_training.gff  --out /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_B_1/plus_hmm.gff  --mod /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_2/ES_A_2.mod 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Fri May 24 07:27:35 2024] 338 contigs in list
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:24 2024] ln -sf /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_A_2/ES_A_2.mod  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run/ES_B_1/prev.mod
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:37 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/parse_set.pl --section ES_B --cfg  /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg  --v
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:38 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section start_ATG   --format INI
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:39 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TAA    --format TERM_TAA
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:39 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TAG    --format TERM_TAG
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:39 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section stop_TGA    --format TERM_TGA
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:39 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section donor_GT    --format DONOR_0    --phase 0 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:40 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section acceptor_AG --format ACCEPTOR_0 --phase 0 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:40 2024]  cat  GT.mat > donor.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:40 2024]  cat  AG.mat > acceptor.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:40 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section donor_GT    --format DONOR_1    --phase 1 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:41 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section acceptor_AG --format ACCEPTOR_1 --phase 1 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:41 2024]  cat  GT.mat >> donor.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:41 2024]  cat  AG.mat >> acceptor.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:41 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section donor_GT    --format DONOR_2    --phase 2 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:42 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/make_nt_freq_mat.pl --cfg /data/home/zhou3lab/sq/project/seahorse/06.genomeAnno/02.funannotate/04.fun_HJ/fun/predict_misc/genemark/run.cfg --section acceptor_AG --format ACCEPTOR_2 --phase 2 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:42 2024]  cat  GT.mat >> donor.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:42 2024]  cat  AG.mat >> acceptor.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:42 2024]  mv donor.mat     GT.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:42 2024]  mv acceptor.mat  AG.mat 
/data/home/zhou3lab/sq/tools2/gmes_linux_64_4/gmes_petap.pl : [Sun May 26 06:45:49 2024] /data/home/zhou3lab/sq/tools2/gmes_linux_64_4/probuild --cod cod.seq --non non.seq --mkmod_euk mkch    --MKCHAIN_L_MARGING 0  --MKCHAIN_R_MARGING 0  --MKCHAIN_PSEUDOCOUNTS 1  --MKCHAIN_PRECISION 8 --revcomp_non  --ORDM 5

any suggestion would be helpful.