

[93m[1m[4mStarting Captus-assembly: EXTRACT[0m [2m(2024-08-13 05:40:27)[0m
[2m    Welcome to the marker extraction step of Captus-assembly. In this step,[0m
[2mCaptus will use Scipio to search within your FASTA assemblies and recover any[0m
[2mset of reference proteins provided through '--nuc_refs', '--ptd_refs', and/or '[0m
[2m--mit_refs'. Captus includes some reference protein sets to work with Plants[0m
[2mlike the 'Angiosperms353' protein set for nuclear genes, and two organellar[0m
[2mprotein reference sets 'SeedPlantsPTD' for plastids, and 'SeedPlantsMIT' for[0m
[2mmitochondria.[0m
[2m    If you have references that are not proteins (e.g. non-coding regions, gene[0m
[2msequences including introns, full mRNAs, etc.) You can provide these[0m
[2mmiscellaneous DNA references with '--dna_refs' and Captus will use BLAT to find[0m
[2mand extract matches in your assemblies.[0m
[2m    Finally, if you want to explore the usefulness of the contigs that were not[0m
[2mhit by any protein or other DNA references after the Captus' extraction[0m
[2mprocess, or simply if you do not have reference sets to test, you can try the[0m
[2moption '--cluster_leftovers' to attempt sequence clustering across samples in[0m
[2morder to discover homologous markers.[0m
[2m    For more information, please see https://github.com/edgardomortiz/Captus[0m

           Captus version: [1mv1.0.1[0m
                  Command: [1m/dmz/home/vferreira/.conda/envs/captus/bin/captus_assembly extract -a 02_assemblies -n probe.fasta[0m
                 Max. RAM: [1m747.7GB[0m [2m(out of 755.3GB)[0m
             Max. Threads: [1m72[0m [2m(out of 72)[0m

             Dependencies:
                Scipio   : [1mv1.4.1[0m [32m[1mOK[0m
                â”œâ”€BioPerl: [1mv1.7.8[0m [32m[1mOK[0m
                â””â”€YAML   : [1mv1.30[0m [32m[1mOK[0m
                BLAT     : [1mv37x1[0m [32m[1mOK[0m
                MMseqs2  : [2mnot used[0m
                MAFFT    : [2mnot used[0m

         Python libraries:
                    numpy: [1mv2.0.0[0m [32m[1mOK[0m
                   pandas: [1mv2.2.2[0m [32m[1mOK[0m
                   plotly: [1mv5.22.0[0m [32m[1mOK[0m

    Captus assemblies dir: [1m/dmz/home/vferreira/captus_lycidae_working2/02_assemblies[0m
[32m[1m                           VALID Captus assemblies directory with 27 samples and 27 'assembly.fasta' files[0m

   Total assemblies found: [1m27[0m

         Output directory: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions[0m
                           [2mOutput directory already exists and files may be overwritten[0m



[93m[1m[4mProtein and DNA Markers Extraction from FASTA assemblies[0m [2m(2024-08-13 05:40:39)[0m
[2m    Now Captus will search within your FASTA assemblies for the set of[0m
[2mreference proteins provided by '--nuc_refs', '--ptd_refs', and/or '--mit_refs'[0m
[2mand extract the sequences both in nucleotide and translated to aminoacid using[0m
[2mthe specified '--nuc_transtable', '--ptd_transtable' and '--mit_transtable'[0m
[2mrespectively.[0m
[2m    Additionally, miscellaneous DNA references provided with '--dna_refs' will[0m
[2malso be extracted.[0m

Verifying protein reference sets...
Translated '[1mprobe.fasta[0m' using Genetic Code: [1m1[0m [8.103s]

[1m          PROTEIN OPTIONS:[0m
  Max. loci for Scipio x2: [1m2000[0m
  Predict dubious introns: [1mFalse[0m
   Concurrent extractions: [1m27[0m
       RAM per extraction: [1m27.7GB[0m
   Threads per extraction: [1m2[0m

[1m         Nuclear proteins:[0m
                reference: [1m/dmz/home/vferreira/captus_lycidae_working2/probe.captus.faa[0m [2m(Translated from[0m [2mprobe.fasta[0m[2m)[0m
           reference info: [1m2,260 loci, 40,190 sequences [0m[2m(loci names found, detected multiple sequences per locus)[0m
                min_score: [1m0.13[0m
             min_identity: [1m65[0m
             min_coverage: [1m20[0m
        translation table: [1m1[0m

[1m      Plastidial proteins:[0m
                reference: [2mnot used[0m

[1m   Mitochondrial proteins:[0m
                reference: [2mnot used[0m


[1mMISCELLANEOUS DNA OPTIONS:[0m
                reference: [2mnot used[0m


[1m           OUTPUT OPTIONS:[0m
            Max. paralogs: [1m-1[0m [2m(Keep all paralogs)[0m
 Max. separate loci files: [1m0[0m [2m(Do not write separate loci files per sample)[0m
          Overwrite files: [1mFalse[0m
           Keep all files: [1mFalse[0m

       Samples to process: [1m27[0m
   Extractions to process: [1m27 protein[0m and [1m0 nucleotide[0m

         Nuclear proteins: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/[Sample_name]__captus-ext/[0m[1m01_coding_NUC[0m
     Annotated assemblies: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/[Sample_name]__captus-ext/06_assembly_annotated[0m
                           [2m(These output directories will be created for each sample)[0m

 Paths to references used: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/captus-assembly_extract.refs.json[0m

[1mExtracting protein-coding markers with Scipio:[0m

  0%|                                            | 0/27 [00:00<?, ?extraction/s]
                                                                                

  0%|                                            | 0/27 [00:00<?, ?extraction/s]
  4%|â–ˆâ–Ž                                  | 1/27 [00:00<00:02,  9.01extraction/s]
                                                                                

  4%|â–ˆâ–Ž                                  | 1/27 [00:00<00:02,  9.01extraction/s]
                                                                                

  7%|â–ˆâ–ˆâ–‹                                 | 2/27 [00:00<00:02,  9.01extraction/s]
                                                                                

 11%|â–ˆâ–ˆâ–ˆâ–ˆ                                | 3/27 [00:00<00:02,  9.01extraction/s]
                                                                                

 15%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                              | 4/27 [00:00<00:02,  9.01extraction/s]
 19%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                             | 5/27 [00:00<00:00, 22.90extraction/s]
                                                                                

 19%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                             | 5/27 [00:00<00:00, 22.90extraction/s]
                                                                                

 22%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                            | 6/27 [00:00<00:00, 22.90extraction/s]
                                                                                

 26%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                          | 7/27 [00:00<00:00, 22.90extraction/s]
                                                                                

 30%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                         | 8/27 [00:00<00:00, 22.90extraction/s]
 33%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                        | 9/27 [00:00<00:00, 24.36extraction/s]
                                                                                

 33%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                        | 9/27 [00:00<00:00, 24.36extraction/s]
                                                                                

 37%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‰                      | 10/27 [00:00<00:00, 24.36extraction/s]
                                                                                

 41%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                    | 11/27 [00:00<00:00, 24.36extraction/s]
 44%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ                   | 12/27 [00:00<00:00, 26.05extraction/s]
                                                                                

 44%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ                   | 12/27 [00:00<00:00, 26.05extraction/s]
                                                                                

 48%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š                  | 13/27 [00:00<00:00, 26.05extraction/s]
                                                                                

 52%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–                | 14/27 [00:00<00:00, 26.05extraction/s]
                                                                                

 56%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–               | 15/27 [00:00<00:00, 26.05extraction/s]
 59%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹              | 16/27 [00:00<00:00, 28.28extraction/s]
                                                                                

 59%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹              | 16/27 [00:00<00:00, 28.28extraction/s]
                                                                                

 63%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ             | 17/27 [00:00<00:00, 28.28extraction/s]
                                                                                

 67%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž           | 18/27 [00:00<00:00, 28.28extraction/s]
                                                                                

 70%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹          | 19/27 [00:00<00:00, 28.28extraction/s]
                                                                                

 74%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‰         | 20/27 [00:00<00:00, 28.28extraction/s]
 78%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–       | 21/27 [00:00<00:00, 31.85extraction/s]
                                                                                

 78%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–       | 21/27 [00:00<00:00, 31.85extraction/s]
                                                                                

 81%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ      | 22/27 [00:00<00:00, 31.85extraction/s]
                                                                                

 85%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š     | 23/27 [00:00<00:00, 31.85extraction/s]
                                                                                

 89%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ    | 24/27 [00:00<00:00, 31.85extraction/s]
 93%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–  | 25/27 [00:00<00:00, 31.63extraction/s]
                                                                                

 93%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–  | 25/27 [00:00<00:00, 31.63extraction/s]
                                                                                

 96%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹ | 26/27 [00:00<00:00, 31.63extraction/s]
100%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ| 27/27 [00:00<00:00, 28.40extraction/s]
[2m'DexorisSRR8739606': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739607': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739605_Cauti': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0091': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0051': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0061': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0062': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739602': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739617': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739620': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739610': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739608': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739616': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739601': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739619': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739604': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739615': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739614': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739611': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739612': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739613': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739618': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739599': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739603': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739600': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739609': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'ENT957a_S11_L001': extraction of nuclear genes SKIPPED (output files already exist)[0m
[1m â””â”€â†’ Protein-coding markers: finished processing for 27 extraction(s) [0.998s][0m

[1mMerging GFFs, summarizing recovery stats, and cleaning up:[0m

  0%|                                                | 0/27 [00:00<?, ?sample/s]
                                                                                

  0%|                                                | 0/27 [00:00<?, ?sample/s]
                                                                                

  4%|â–ˆâ–                                     | 1/27 [00:00<00:00, 177.08sample/s]
                                                                                

  7%|â–ˆâ–ˆâ–‰                                    | 2/27 [00:00<00:00, 312.10sample/s]
                                                                                

 11%|â–ˆâ–ˆâ–ˆâ–ˆâ–Ž                                  | 3/27 [00:00<00:00, 454.31sample/s]
                                                                                

 15%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š                                 | 4/27 [00:00<00:00, 589.54sample/s]
                                                                                

 19%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–                               | 5/27 [00:00<00:00, 678.32sample/s]
                                                                                

 22%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                              | 6/27 [00:00<00:00, 795.48sample/s]
                                                                                

 26%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                             | 7/27 [00:00<00:00, 895.86sample/s]
                                                                                

 30%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                          | 8/27 [00:00<00:00, 1001.36sample/s]
                                                                                

 33%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                         | 9/27 [00:00<00:00, 1102.89sample/s]
                                                                                

 37%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                       | 10/27 [00:00<00:00, 1187.85sample/s]
                                                                                

 41%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                      | 11/27 [00:00<00:00, 1279.71sample/s]
                                                                                

 44%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–                    | 12/27 [00:00<00:00, 1362.12sample/s]
                                                                                

 48%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š                   | 13/27 [00:00<00:00, 1444.47sample/s]
                                                                                

 52%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–                  | 14/27 [00:00<00:00, 27.51sample/s]
 56%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                 | 15/27 [00:00<00:00, 29.47sample/s]
                                                                                

 56%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                 | 15/27 [00:00<00:00, 29.47sample/s]
                                                                                

 59%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                | 16/27 [00:00<00:00, 29.47sample/s]
                                                                                

 63%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ              | 17/27 [00:00<00:00, 29.47sample/s]
                                                                                

 67%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ             | 18/27 [00:00<00:00, 29.47sample/s]
                                                                                

 70%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–           | 19/27 [00:03<00:00, 29.47sample/s]
 74%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‰          | 20/27 [00:03<00:01,  5.03sample/s]
                                                                                

 74%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‰          | 20/27 [00:04<00:01,  5.03sample/s]
                                                                                

 78%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž        | 21/27 [00:05<00:01,  5.03sample/s]
 81%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š       | 22/27 [00:05<00:01,  2.93sample/s]
                                                                                

 81%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š       | 22/27 [00:05<00:01,  2.93sample/s]
 85%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–     | 23/27 [00:05<00:01,  3.02sample/s]
                                                                                

 85%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–     | 23/27 [00:07<00:01,  3.02sample/s]
 89%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹    | 24/27 [00:07<00:01,  1.88sample/s]
                                                                                

 89%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹    | 24/27 [00:11<00:01,  1.88sample/s]
 93%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ   | 25/27 [00:11<00:02,  1.03s/sample]
                                                                                

 93%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ   | 25/27 [42:32<00:02,  1.03s/sample]
 96%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ | 26/27 [42:32<07:33, 453.15s/sample]
                                                                                

 96%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹ | 26/27 [1:16:54<07:33, 453.15s/sample]
100%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ| 27/27 [1:16:54<00:00, 779.29s/sample]
100%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ| 27/27 [1:16:54<00:00, 170.92s/sample]
[2m'SRR8739617': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'PD0091': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'PD0062': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739602': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739620': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739616': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739619': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739612': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739604': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739615': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739603': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739599': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739600': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'ENT957a_S11_L001': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739601': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'PD0061': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'PD0051': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[2m'SRR8739613': cleanup and merging of GFFs and stats SKIPPED (output files already exist)[0m
[31m'SRR8739607': GFF was empty, marker extraction FAILED [0.512s][0m
'SRR8739609': GFF annotations and recovery stats merged, unnecessary files removed [3.214s]
'SRR8739618': GFF annotations and recovery stats merged, unnecessary files removed [4.803s]
'SRR8739611': GFF annotations and recovery stats merged, unnecessary files removed [5.444s]
'SRR8739614': GFF annotations and recovery stats merged, unnecessary files removed [5.678s]
'SRR8739608': GFF annotations and recovery stats merged, unnecessary files removed [7.614s]
'SRR8739610': GFF annotations and recovery stats merged, unnecessary files removed [11.402s]
'SRR8739605_Cauti': GFF annotations and recovery stats merged, unnecessary files removed [42m 31.6s (2551.590s)]
'DexorisSRR8739606': GFF annotations and recovery stats merged, unnecessary files removed [1h 16m 52.7s (4612.652s)]
[1m â””â”€â†’ Merged GFF and summary recovery stats created for 27 sample(s) [1h 16m 54.9s (4614.888s)][0m



[93m[1m[4mClustering and Extracting Markers Across Samples with MMseqs2/BLAT[0m [2m(2024-08-13 06:57:43)[0m
[2m    Now Captus will cluster the assembly sequences across samples to discover[0m
[2mhomologous markers. If protein and/or miscellaneous DNA references sequences[0m
[2mwere extracted in the previous step, the[0m
[2m'06_assembly_annotated/leftover_contigs.fasta.gz' files from each sample will[0m
[2mbe used for clustering, otherwise the '01_assembly/assembly.fasta' files are[0m
[2mused. USE WITH CAUTION: Clustering time and/or success will depend on the size[0m
[2mof your assembly files, it should be safe to use if you assembled captured[0m
[2mdata, RNAseq reads, or even genome skimming data.[0m
[2m    After clustering has been completed, only the clusters with at least '--[0m
[2mcl_min_samples' will be considered and a single representative sequence from[0m
[2meach cluster will be selected to create a new reference file to perform a final[0m
[2mDNA marker extraction across all samples. The extraction of these new markers[0m
[2mis done with the same settings chosen for miscellaneous DNA markers.[0m

[31mSkipping clustering step... (to enable use '--cluster_leftovers', and verify that all the software dependencies are correctly installed)[0m



[93m[1m[4mStatistics Summarization[0m [2m(2024-08-13 06:57:43)[0m
[2m    Now Captus will collect the extraction statistics from each sample to[0m
[2mcompile a comprehensive table and a HTML report for visualization of extraction[0m
[2mstatistics.[0m

    Extraction statistics: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/captus-assembly_extract.stats.tsv[0m

[2m    Generating Marker Extraction report...[0m

        Extraction report: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/captus-assembly_extract.report.html[0m
                           [2m[2mReport generated in 5.944s[0m[0m



[93m[1m[4mCaptus-assembly: EXTRACT -> successfully completed [1h 17m 23.4s (4643.393s)][0m [2m(2024-08-13 06:57:51)[0m



[93m[1m[4mStarting Captus-assembly: EXTRACT[0m [2m(2024-08-13 09:22:17)[0m
[2m    Welcome to the marker extraction step of Captus-assembly. In this step,[0m
[2mCaptus will use Scipio to search within your FASTA assemblies and recover any[0m
[2mset of reference proteins provided through '--nuc_refs', '--ptd_refs', and/or '[0m
[2m--mit_refs'. Captus includes some reference protein sets to work with Plants[0m
[2mlike the 'Angiosperms353' protein set for nuclear genes, and two organellar[0m
[2mprotein reference sets 'SeedPlantsPTD' for plastids, and 'SeedPlantsMIT' for[0m
[2mmitochondria.[0m
[2m    If you have references that are not proteins (e.g. non-coding regions, gene[0m
[2msequences including introns, full mRNAs, etc.) You can provide these[0m
[2mmiscellaneous DNA references with '--dna_refs' and Captus will use BLAT to find[0m
[2mand extract matches in your assemblies.[0m
[2m    Finally, if you want to explore the usefulness of the contigs that were not[0m
[2mhit by any protein or other DNA references after the Captus' extraction[0m
[2mprocess, or simply if you do not have reference sets to test, you can try the[0m
[2moption '--cluster_leftovers' to attempt sequence clustering across samples in[0m
[2morder to discover homologous markers.[0m
[2m    For more information, please see https://github.com/edgardomortiz/Captus[0m

           Captus version: [1mv1.0.1[0m
                  Command: [1m/dmz/home/vferreira/.conda/envs/captus/bin/captus_assembly extract -a 02_assemblies -n probe.fasta[0m
                 Max. RAM: [1m747.7GB[0m [2m(out of 755.3GB)[0m
             Max. Threads: [1m72[0m [2m(out of 72)[0m

             Dependencies:
                Scipio   : [1mv1.4.1[0m [32m[1mOK[0m
                â”œâ”€BioPerl: [1mv1.7.8[0m [32m[1mOK[0m
                â””â”€YAML   : [1mv1.30[0m [32m[1mOK[0m
                BLAT     : [1mv37x1[0m [32m[1mOK[0m
                MMseqs2  : [2mnot used[0m
                MAFFT    : [2mnot used[0m

         Python libraries:
                    numpy: [1mv2.0.0[0m [32m[1mOK[0m
                   pandas: [1mv2.2.2[0m [32m[1mOK[0m
                   plotly: [1mv5.22.0[0m [32m[1mOK[0m

    Captus assemblies dir: [1m/dmz/home/vferreira/captus_lycidae_working2/02_assemblies[0m
[32m[1m                           VALID Captus assemblies directory with 27 samples and 27 'assembly.fasta' files[0m

   Total assemblies found: [1m27[0m

         Output directory: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions[0m
                           [2mOutput directory already exists and files may be overwritten[0m



[93m[1m[4mProtein and DNA Markers Extraction from FASTA assemblies[0m [2m(2024-08-13 09:22:18)[0m
[2m    Now Captus will search within your FASTA assemblies for the set of[0m
[2mreference proteins provided by '--nuc_refs', '--ptd_refs', and/or '--mit_refs'[0m
[2mand extract the sequences both in nucleotide and translated to aminoacid using[0m
[2mthe specified '--nuc_transtable', '--ptd_transtable' and '--mit_transtable'[0m
[2mrespectively.[0m
[2m    Additionally, miscellaneous DNA references provided with '--dna_refs' will[0m
[2malso be extracted.[0m

Verifying protein reference sets...
Translated '[1mprobe.fasta[0m' using Genetic Code: [1m1[0m [7.951s]

[1m          PROTEIN OPTIONS:[0m
  Max. loci for Scipio x2: [1m2000[0m
  Predict dubious introns: [1mFalse[0m
   Concurrent extractions: [1m27[0m
       RAM per extraction: [1m27.7GB[0m
   Threads per extraction: [1m2[0m

[1m         Nuclear proteins:[0m
                reference: [1m/dmz/home/vferreira/captus_lycidae_working2/probe.captus.faa[0m [2m(Translated from[0m [2mprobe.fasta[0m[2m)[0m
           reference info: [1m2,260 loci, 40,190 sequences [0m[2m(loci names found, detected multiple sequences per locus)[0m
                min_score: [1m0.13[0m
             min_identity: [1m65[0m
             min_coverage: [1m20[0m
        translation table: [1m1[0m

[1m      Plastidial proteins:[0m
                reference: [2mnot used[0m

[1m   Mitochondrial proteins:[0m
                reference: [2mnot used[0m


[1mMISCELLANEOUS DNA OPTIONS:[0m
                reference: [2mnot used[0m


[1m           OUTPUT OPTIONS:[0m
            Max. paralogs: [1m-1[0m [2m(Keep all paralogs)[0m
 Max. separate loci files: [1m0[0m [2m(Do not write separate loci files per sample)[0m
          Overwrite files: [1mFalse[0m
           Keep all files: [1mFalse[0m

       Samples to process: [1m27[0m
   Extractions to process: [1m27 protein[0m and [1m0 nucleotide[0m

         Nuclear proteins: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/[Sample_name]__captus-ext/[0m[1m01_coding_NUC[0m
     Annotated assemblies: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/[Sample_name]__captus-ext/06_assembly_annotated[0m
                           [2m(These output directories will be created for each sample)[0m

 Paths to references used: [1m/dmz/home/vferreira/captus_lycidae_working2/03_extractions/captus-assembly_extract.refs.json[0m

[1mExtracting protein-coding markers with Scipio:[0m

  0%|                                            | 0/27 [00:00<?, ?extraction/s]
                                                                                

  0%|                                            | 0/27 [00:00<?, ?extraction/s]
  4%|â–ˆâ–Ž                                  | 1/27 [00:00<00:03,  8.56extraction/s]
                                                                                

  4%|â–ˆâ–Ž                                  | 1/27 [00:00<00:03,  8.56extraction/s]
                                                                                

  7%|â–ˆâ–ˆâ–‹                                 | 2/27 [00:00<00:02,  8.56extraction/s]
 11%|â–ˆâ–ˆâ–ˆâ–ˆ                                | 3/27 [00:00<00:01, 14.23extraction/s]
                                                                                

 11%|â–ˆâ–ˆâ–ˆâ–ˆ                                | 3/27 [00:00<00:01, 14.23extraction/s]
                                                                                

 15%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                              | 4/27 [00:00<00:01, 14.23extraction/s]
                                                                                

 19%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                             | 5/27 [00:00<00:01, 14.23extraction/s]
 22%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                            | 6/27 [00:00<00:01, 20.62extraction/s]
                                                                                

 22%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                            | 6/27 [00:00<00:01, 20.62extraction/s]
                                                                                

 26%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                          | 7/27 [00:00<00:00, 20.62extraction/s]
                                                                                

 30%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹                         | 8/27 [00:00<00:00, 20.62extraction/s]
 33%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                        | 9/27 [00:00<00:00, 24.03extraction/s]
                                                                                

 33%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ                        | 9/27 [00:00<00:00, 24.03extraction/s]
                                                                                

 37%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‰                      | 10/27 [00:00<00:00, 24.03extraction/s]
                                                                                

 41%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž                    | 11/27 [00:00<00:00, 24.03extraction/s]
                                                                                

 44%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ                   | 12/27 [00:00<00:00, 24.03extraction/s]
 48%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š                  | 13/27 [00:00<00:00, 27.49extraction/s]
                                                                                

 48%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š                  | 13/27 [00:00<00:00, 27.49extraction/s]
                                                                                

 52%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–                | 14/27 [00:00<00:00, 27.49extraction/s]
                                                                                

 56%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–               | 15/27 [00:00<00:00, 27.49extraction/s]
                                                                                

 59%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹              | 16/27 [00:00<00:00, 27.49extraction/s]
 63%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ             | 17/27 [00:00<00:00, 29.77extraction/s]
                                                                                

 63%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ             | 17/27 [00:00<00:00, 29.77extraction/s]
                                                                                

 67%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Ž           | 18/27 [00:00<00:00, 29.77extraction/s]
                                                                                

 70%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹          | 19/27 [00:00<00:00, 29.77extraction/s]
                                                                                

 74%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‰         | 20/27 [00:00<00:00, 29.77extraction/s]
 78%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–       | 21/27 [00:00<00:00, 31.25extraction/s]
                                                                                

 78%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–       | 21/27 [00:00<00:00, 31.25extraction/s]
                                                                                

 81%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Œ      | 22/27 [00:00<00:00, 31.25extraction/s]
                                                                                

 85%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š     | 23/27 [00:00<00:00, 31.25extraction/s]
                                                                                

 89%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆ    | 24/27 [00:00<00:00, 31.25extraction/s]
 93%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–  | 25/27 [00:00<00:00, 32.12extraction/s]
                                                                                

 93%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–  | 25/27 [00:00<00:00, 32.12extraction/s]
 96%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–‹ | 26/27 [00:19<00:00, 32.12extraction/s][2m'DexorisSRR8739606': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739605_Cauti': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0091': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0051': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0061': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'PD0062': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739602': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739617': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739620': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739610': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739608': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739616': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739601': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739619': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739604': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739615': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739614': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739611': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739612': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739613': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739618': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739599': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739603': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739600': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'SRR8739609': extraction of nuclear genes SKIPPED (output files already exist)[0m
[2m'ENT957a_S11_L001': extraction of nuclear genes SKIPPED (output files already exist)[0m
concurrent.futures.process._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/concurrent/futures/process.py", line 263, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/extract.py", line 1339, in scipio_coding
    final_models = scipio_yaml_to_dict(yaml_final_file, min_score, min_identity,
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/bioformats.py", line 2321, in scipio_yaml_to_dict
    model = parse_model(yaml[prot][yaml_model],
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/bioformats.py", line 2304, in parse_model
    mismatch_rate      = len(set(mod["mismatches"])) / prot_len_matched
                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
ZeroDivisionError: division by zero
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/dmz/home/vferreira/.conda/envs/captus/bin/captus_assembly", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/captus_assembly.py", line 1424, in main
    CaptusAssembly()
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/captus_assembly.py", line 90, in __init__
    getattr(self, args.command)()
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/captus_assembly.py", line 1074, in extract
    extract(full_command, args)
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/extract.py", line 505, in extract
    tqdm_parallel_nested_run(scipio_coding, scipio_params, d_msg, f_msg,
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/site-packages/captus/misc.py", line 158, in tqdm_parallel_nested_run
    result = future.result()
             ^^^^^^^^^^^^^^^
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/dmz/home/vferreira/.conda/envs/captus/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
ZeroDivisionError: division by zero

 96%|â–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–ˆâ–Š | 26/27 [3:30:15<08:05, 485.20s/extraction]