"gnomon_filter_models" can't proceed further

[tiantian-chen]

I'm currently stuck at the "gnomon_filter_models" step and can't proceed further.

[30/dbd19a] ega…_summary:gnomon_report (5) | 16 of 16 ✔
[b3/c05aaa] ega…evidence_summary:gpx_qdump | 1 of 1 ✔
[e3/5bae53] ega…nce_summary:create_reports | 1 of 1 ✔
[56/101664] ega…nce_summary:gnomon_summary | 1 of 1 ✔
[89/e677d6] ega…plane:fetch_swiss_prot_asn | 1 of 1 ✔
[8b/d64527] ega…n_plane:get_swiss_prot_ids | 1 of 1 ✔
[71/8532cb] ega…pare:prot_gnomon_prepare_p | 1 of 1 ✔
[3c/1c7857] ega…nd_worker:run_diamond_egap | 1 of 1 ✔
[1c/4d44e9] ega…protein_filter_replacement | 1 of 1 ✔
[9e/2457e8] ega…cores:gnomon_filter_models | 0 of 1, retries: 5
[f4/99551d] ega…builder:annot_builder_main | 1 of 1 ✔
[4c/6eff5d] ega…_plane:print_fake_lxr_data | 1 of 1 ✔
[8a/961f5b] ega…:fetch_ortholog_references | 1 of 1 ✔
[a1/059f2b] ega…ext_genome:get_genome_info | 1 of 1 ✔
[df/ce4663] ega…_proteins:convert_proteins | 1 of 1 ✔
[aa/c70397] ega…ogy_plane:get_prot_ref_ids | 1 of 1 ✔
Plus 15 more processes waiting for tasks…
[b5/12a636] NOTE: Process egapx:gnomon_plane:gnomon_add_filtering_scores:gnomon_filter_models failed -- Execution is retried (5)

Below are my chromosome information and some log information.

`cat yanmaicaon2.yaml
genome: /share/org/YZWL/yzwl_qinzy/soft/new_egapx/egapx/modifiedyanmaicaoclean1.fasta
taxid: 4589
locus_tag_prefix: Thinopyrumponticum
short_reads: /share/org/YZWL/yzwl_qinzy/soft/new_egapx/egapx/new_tra.txt

cat /share/org/YZWL/yzwl_qinzy/soft/new_egapx/egapx/new_tra.txt
SRR202506291 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d10hA_R1.fa
SRR202506291 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d10hA_R2.fa
SRR202506292 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d112hA_R1.fa
SRR202506292 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d112hA_R2.fa
SRR202506293 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d124hA_R1.fa
SRR202506293 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d124hA_R2.fa
SRR202506294 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d148hA_R1.fa
SRR202506294 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d148hA_R2.fa
SRR202506295 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d172hA_R1.fa
SRR202506295 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d172hA_R2.fa
SRR202506296 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d17dA_R1.fa
SRR202506296 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d17dA_R2.fa
SRR202506297 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d20hA_R1.fa
SRR202506297 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d20hA_R2.fa
SRR202506298 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d212hA_R1.fa
SRR202506298 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d212hA_R2.fa
SRR202506299 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d224hA_R1.fa
SRR202506299 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d224hA_R2.fa
SRR2025062910 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d248hA_R1.fa
SRR2025062910 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d248hA_R2.fa
SRR2025062911 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d272hA_R1.fa
SRR2025062911 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d272hA_R2.fa
SRR2025062912 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d27dA_R1.fa
SRR2025062912 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d27dA_R2.fa
SRR2025062913 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d30hA_R1.fa
SRR2025062913 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d30hA_R2.fa
SRR2025062914 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d312hA_R1.fa
SRR2025062914 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d312hA_R2.fa
SRR2025062915 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d324hA_R1.fa
SRR2025062915 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d324hA_R2.fa
SRR2025062916 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d348hA_R1.fa
SRR2025062916 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d348hA_R2.fa
SRR2025062917 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d372hA_R1.fa
SRR2025062917 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d372hA_R2.fa
SRR2025062918 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d37dA_R1.fa
SRR2025062918 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/d37dA_R2.fa
SRR2025062921 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p212haA_R1.fa
SRR2025062921 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p212haA_R2.fa
SRR2025062924 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p224haA_R1.fa
SRR2025062924 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p224haA_R2.fa
SRR2025062927 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p248haA_R1.fa
SRR2025062927 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p248haA_R2.fa
SRR2025062930 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p272haA_R1.fa
SRR2025062930 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p272haA_R2.fa
SRR2025070212 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p27daA_R1.fa
SRR2025070212 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p27daA_R2.fa
SRR202507022 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p48haA_R1.fa
SRR202507022 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p48haA_R2.fa
SRR202507025 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p72haA_R1.fa
SRR202507025 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p72haA_R2.fa
SRR202507028 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p7daA_R1.fa
SRR202507028 /share/org/YZWL/yzwl_qinzy/anno_qzy/RNA-seq/new_fa/p7daA_R2.fa

`

length.txt

[murphyte]

I see this is another very large genome (33.6 Gbp), similar to #169, although this one is proceeding a bit further.

Please post the nextflow.log and run.trace.txt files.
Also, how many lines are in the GNOMON/new_quality_report.txt file? I think that should be in your main output directory, but if not, look in nextflow/run.trace.txt for egapx:convert_summary_files:run_convert_summary_files, and look in its work directory.

[pstrope]

Your task maybe failing due to not enough time. To increase the time limit for gnomon_filter_models, edit this file
egapx/nf/subworkflows/ncbi/gnomon/gnomon_add_filtering_scores/main.nf
line 27
to

process gnomon_filter_models {
    label 'long_job'
    input:

Then you can resume the run.