ERROR ~ Error executing process > 'egapx:target_proteins_plane:paf2asn:run_paf2asn (2)'

[MonsterLaplace]

[38/6a9bb5] egapx:setup_genome:get_genome_info [100%] 1 of 1 ✔
[f3/5a65a5] egapx:setup_proteins:convert_proteins [100%] 1 of 1 ✔
[69/a77736] egapx:target_proteins_plane:miniprot:split_proteins [100%] 1 of 1 ✔
[71/5b7d71] egapx:target_proteins_plane:miniprot:run_miniprot (8) [ 53%] 7 of 13
[36/2933fd] egapx:target_proteins_plane:paf2asn:run_paf2asn (3) [ 68%] 15 of 22, failed: 15, retries: 15
[- ] egapx:target_proteins_plane:best_aligned_prot:run_best_aligned_prot -
[- ] egapx:target_proteins_plane:align_filter_sa:run_align_filter_sa -
[- ] egapx:target_proteins_plane:align_sort_sa:run_align_sort -
[9f/01bb60] egapx:rnaseq_short_plane:star_index:build_index [ 0%] 0 of 1
[- ] egapx:rnaseq_short_plane:star:run_star -
[- ] egapx:rnaseq_short_plane:bam_strandedness:rnaseq_divide_by_strandedness -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:calc_assembly_sizes -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:merge_prepare -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:merge -
[- ] egapx:rnaseq_short_plane:bam2asn:convert -
[- ] egapx:rnaseq_short_plane:rnaseq_collapse:generate_jobs -
[- ] egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse -
[- ] egapx:rnaseq_short_plane:rnaseq_collapse:run_gpx_make_outputs -
[- ] egapx:gnomon_plane:chainer:run_align_sort -
[- ] egapx:gnomon_plane:chainer:generate_jobs -
[- ] egapx:gnomon_plane:chainer:run_chainer -
[- ] egapx:gnomon_plane:chainer:run_gpx_make_outputs -
[- ] egapx:gnomon_plane:gnomon_wnode:gpx_qsubmit -
[- ] egapx:gnomon_plane:gnomon_wnode:annot -
[- ] egapx:gnomon_plane:gnomon_wnode:gpx_qdump -
[90/65b963] egapx:annot_proc_plane:fetch_swiss_prot_asn [100%] 1 of 1 ✔
[b0/20cd98] egapx:annot_proc_plane:get_swiss_prot_ids [100%] 1 of 1 ✔
[- ] egapx:annot_proc_plane:prot_gnomon_prepare:prot_gnomon_prepare_p -
[- ] egapx:annot_proc_plane:diamond_worker:run_diamond_egap -
[- ] egapx:annot_proc_plane:best_protein_hits:run_protein_filter_replacement -
[- ] egapx:annot_proc_plane:gnomon_biotype:run_gnomon_biotype -
[07/b780ee] egapx:annot_proc_plane:annot_builder:annot_builder_main [100%] 1 of 1 ✔
[- ] egapx:annot_proc_plane:annot_builder:annot_builder_input -
[- ] egapx:annot_proc_plane:annot_builder:annot_builder_run -
[6d/04e82c] egapx:annot_proc_plane:print_fake_lxr_data [100%] 1 of 1 ✔
[94/7897e1] egapx:annot_proc_plane:orthology_plane:fetch_ortholog_references [100%] 1 of 1 ✔
[a1/c4cd29] egapx:annot_proc_plane:orthology_plane:setup_ext_genome:get_genome_info [ 0%] 0 of 1
[a4/f87219] egapx:annot_proc_plane:orthology_plane:setup_ext_proteins:convert_proteins [100%] 1 of 1 ✔
[ae/58f967] egapx:annot_proc_plane:orthology_plane:get_prot_ref_ids [100%] 1 of 1 ✔
Plus 9 more processes waiting for tasks…
[69/f46aad] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (5) terminated with an error exit status (3) -- Execution is retried (2)
[4f/92fe24] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (2) terminated with an error exit status (3) -- Execution is retried (3)
[fa/0b9c09] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (4) terminated with an error exit status (3) -- Execution is retried (2)
[a6/252d2e] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (6) terminated with an error exit status (3) -- Execution is retried (2)
[1d/f402a2] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (1) terminated with an error exit status (3) -- Execution is retried (3)
executor > local (47)
[38/6a9bb5] egapx:setup_genome:get_genome_info [100%] 1 of 1 ✔
[f3/5a65a5] egapx:setup_proteins:convert_proteins [100%] 1 of 1 ✔
[69/a77736] egapx:target_proteins_plane:miniprot:split_proteins [100%] 1 of 1 ✔
[23/7a865c] egapx:target_proteins_plane:miniprot:run_miniprot (13) [ 53%] 7 of 13
[23/1a2cad] egapx:target_proteins_plane:paf2asn:run_paf2asn (2) [ 72%] 16 of 22, failed: 16, retries: 15
[- ] egapx:target_proteins_plane:best_aligned_prot:run_best_aligned_prot -
[- ] egapx:target_proteins_plane:align_filter_sa:run_align_filter_sa -
[- ] egapx:target_proteins_plane:align_sort_sa:run_align_sort -
[9f/01bb60] egapx:rnaseq_short_plane:star_index:build_index [ 0%] 0 of 1
[- ] egapx:rnaseq_short_plane:star:run_star -
[- ] egapx:rnaseq_short_plane:bam_strandedness:rnaseq_divide_by_strandedness -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:calc_assembly_sizes -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:merge_prepare -
[- ] egapx:rnaseq_short_plane:bam_bin_and_sort:merge -
[- ] egapx:rnaseq_short_plane:bam2asn:convert -
[- ] egapx:rnaseq_short_plane:rnaseq_collapse:generate_jobs -
[- ] egapx:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse -
[- ] egapx:rnaseq_short_plane:rnaseq_collapse:run_gpx_make_outputs -
[- ] egapx:gnomon_plane:chainer:run_align_sort -
[- ] egapx:gnomon_plane:chainer:generate_jobs -
[- ] egapx:gnomon_plane:chainer:run_chainer -
[- ] egapx:gnomon_plane:chainer:run_gpx_make_outputs -
[- ] egapx:gnomon_plane:gnomon_wnode:gpx_qsubmit -
[- ] egapx:gnomon_plane:gnomon_wnode:annot -
[- ] egapx:gnomon_plane:gnomon_wnode:gpx_qdump -
[90/65b963] egapx:annot_proc_plane:fetch_swiss_prot_asn [100%] 1 of 1 ✔
[b0/20cd98] egapx:annot_proc_plane:get_swiss_prot_ids [100%] 1 of 1 ✔
[- ] egapx:annot_proc_plane:prot_gnomon_prepare:prot_gnomon_prepare_p -
[- ] egapx:annot_proc_plane:diamond_worker:run_diamond_egap -
[- ] egapx:annot_proc_plane:best_protein_hits:run_protein_filter_replacement -
[- ] egapx:annot_proc_plane:gnomon_biotype:run_gnomon_biotype -
[07/b780ee] egapx:annot_proc_plane:annot_builder:annot_builder_main [100%] 1 of 1 ✔
[- ] egapx:annot_proc_plane:annot_builder:annot_builder_input -
[- ] egapx:annot_proc_plane:annot_builder:annot_builder_run -
[6d/04e82c] egapx:annot_proc_plane:print_fake_lxr_data [100%] 1 of 1 ✔
[94/7897e1] egapx:annot_proc_plane:orthology_plane:fetch_ortholog_references [100%] 1 of 1 ✔
[a1/c4cd29] egapx:annot_proc_plane:orthology_plane:setup_ext_genome:get_genome_info [ 0%] 0 of 1
[a4/f87219] egapx:annot_proc_plane:orthology_plane:setup_ext_proteins:convert_proteins [100%] 1 of 1 ✔
[ae/58f967] egapx:annot_proc_plane:orthology_plane:get_prot_ref_ids [100%] 1 of 1 ✔
Plus 9 more processes waiting for tasks…
[69/f46aad] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (5) terminated with an error exit status (3) -- Execution is retried (2)
[4f/92fe24] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (2) terminated with an error exit status (3) -- Execution is retried (3)
[fa/0b9c09] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (4) terminated with an error exit status (3) -- Execution is retried (2)
[a6/252d2e] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (6) terminated with an error exit status (3) -- Execution is retried (2)
[1d/f402a2] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (1) terminated with an error exit status (3) -- Execution is retried (3)
[8b/3ea1d9] NOTE: Process egapx:target_proteins_plane:paf2asn:run_paf2asn (3) terminated with an error exit status (3) -- Execution is retried (3)
ERROR ~ Error executing process > 'egapx:target_proteins_plane:paf2asn:run_paf2asn (2)'

Caused by:
Process egapx:target_proteins_plane:paf2asn:run_paf2asn (2) terminated with an error exit status (3)

Command executed:

mkdir -p output
lds2_indexer -source LDS_Index
echo "3.paf" > input.mft
paf2asn -prosplign-refinement -lds2 LDS_Index/lds2.db -nogenbank -input-manifest input.mft -o output/3.asn

Command exit status:
3

Command output:
(empty)

Command error:
Error: (CSeqVectorException::eSeqDataError) CSeqVector_CI: cannot locate segment at 0
Error: (106.16) CException thrown (CSeqVectorException::eSeqDataError) CSeqVector_CI: cannot locate segment at 0
Error: (CSeqVectorException::eSeqDataError) CSeqVector_CI: cannot locate segment at 0
Error: (106.16) Application's execution failed (CSeqVectorException::eSeqDataError) CSeqVector_CI: cannot locate segment at 0

Work dir:
/mnt/z/xb/egapx/Yak_work/23/1a2cad66f5cb35addf399ac5028309

Container:
/mnt/z/xb/egapx/egapx_0.3.1-alpha.sif

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check 'Yak_out/nextflow.log' file for details

[pstrope]

Hi,
Could you please post your input yaml?
What kind of compute environment are you running this on?

[MonsterLaplace]

Hi, Could you please post your input yaml? What kind of compute environment are you running this on?

I guess I found the reason. The genome and RNA-seqs I used is nwely assembled and sequenced by my own, and the annotation process is running on a local server using Singularity as the container. The genome were scaffold by homologous comparing to closely related species using Ragtag and removing redundancies by purge_dups . The assembled genome format is different form the one scaffolding by Hi-C strategy. For example, The gaps in my assembly is represented by 100 "N", but in HiC scaffold genome is 200 "N". The egapx paf2asn program may not recognize the Non-standard format genome correctly.