[2024-01-24 13:08:57,873] [INFO] DFAST_QC pipeline started. [2024-01-24 13:08:57,875] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:08:57,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference [2024-01-24 13:08:59,111] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:08:59,112] [INFO] Task started: Prodigal [2024-01-24 13:08:59,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgf68cec90-db98-4736-aac0-5269c9e12731/GCF_022751215.1_ASM2275121v1_genomic.fna.gz | prodigal -d GCF_022751215.1_ASM2275121v1_genomic.fna/cds.fna -a GCF_022751215.1_ASM2275121v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:09:22,585] [INFO] Task succeeded: Prodigal [2024-01-24 13:09:22,585] [INFO] Task started: HMMsearch [2024-01-24 13:09:22,586] [INFO] Running command: hmmsearch --tblout GCF_022751215.1_ASM2275121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference/reference_markers.hmm GCF_022751215.1_ASM2275121v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:09:22,972] [INFO] Task succeeded: HMMsearch [2024-01-24 13:09:22,974] [INFO] Found 6/6 markers. [2024-01-24 13:09:23,053] [INFO] Query marker FASTA was written to GCF_022751215.1_ASM2275121v1_genomic.fna/markers.fasta [2024-01-24 13:09:23,053] [INFO] Task started: Blastn [2024-01-24 13:09:23,053] [INFO] Running command: blastn -query GCF_022751215.1_ASM2275121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference/reference_markers.fasta -out GCF_022751215.1_ASM2275121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:09:24,311] [INFO] Task succeeded: Blastn [2024-01-24 13:09:24,315] [INFO] Selected 15 target genomes. [2024-01-24 13:09:24,316] [INFO] Target genome list was writen to GCF_022751215.1_ASM2275121v1_genomic.fna/target_genomes.txt [2024-01-24 13:09:24,398] [INFO] Task started: fastANI [2024-01-24 13:09:24,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68cec90-db98-4736-aac0-5269c9e12731/GCF_022751215.1_ASM2275121v1_genomic.fna.gz --refList GCF_022751215.1_ASM2275121v1_genomic.fna/target_genomes.txt --output GCF_022751215.1_ASM2275121v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:10:01,336] [INFO] Task succeeded: fastANI [2024-01-24 13:10:01,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:10:01,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:10:01,348] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold) [2024-01-24 13:10:01,348] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 13:10:01,349] [INFO] DFAST Taxonomy check final result -------------------------------------------------------------------------------- organism_name strain accession taxid species_taxid relation_to_type validated ani matched_fragments total_fragments ani_threshold status Actinomadura litoris strain=NEAU-AAG5 GCA_009733595.1 2678616 2678616 type True 93.0221 2501 2978 95 below_threshold Actinomadura graeca strain=32-07 GCA_019175365.1 2750812 2750812 type True 86.2163 1888 2978 95 below_threshold Actinomadura macra strain=NBRC 14102 GCA_001552215.1 46164 46164 type True 85.6795 1934 2978 95 below_threshold Actinomadura rubrisoli strain=H3C3 GCA_004349215.1 2530368 2530368 type True 85.2481 1769 2978 95 below_threshold Actinomadura roseirufa GCA_900659635.1 2094049 2094049 type True 84.5101 1640 2978 95 below_threshold Actinomadura bangladeshensis strain=DSM 45347 GCA_004348335.1 453573 453573 type True 84.0873 1431 2978 95 below_threshold Actinomadura coerulea strain=JCM 3320 GCA_014648535.1 46159 46159 type True 83.8476 1647 2978 95 below_threshold Actinomadura coerulea strain=DSM 43675 GCA_014208105.1 46159 46159 type True 83.8151 1676 2978 95 below_threshold Actinomadura violacea strain=LCR2-06 GCA_017573465.1 2819934 2819934 type True 83.73 1825 2978 95 below_threshold Actinomadura nitritigenes strain=L46 GCA_017573545.1 134602 134602 type True 83.6663 1790 2978 95 below_threshold Actinomadura geliboluensis strain=A8036 GCA_005889745.1 882440 882440 type True 83.6529 1450 2978 95 below_threshold Actinomadura spongiicola strain=LHW52907 GCA_003432485.1 2303421 2303421 type True 83.2056 1576 2978 95 below_threshold Actinomadura cremea strain=JCM 3308 GCA_014648495.1 1991 1991 type True 82.3891 1610 2978 95 below_threshold Actinomadura parmotrematis strain=PM05-2 GCA_019458805.1 2864039 2864039 type True 81.5545 1424 2978 95 below_threshold Actinomadura rupiterrae strain=DSM 45251 GCA_024172125.1 559627 559627 type True 81.0181 1503 2978 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:10:01,350] [INFO] DFAST Taxonomy check result was written to GCF_022751215.1_ASM2275121v1_genomic.fna/tc_result.tsv [2024-01-24 13:10:01,351] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:10:01,351] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:10:01,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference/checkm_data [2024-01-24 13:10:01,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:10:01,436] [INFO] Task started: CheckM [2024-01-24 13:10:01,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022751215.1_ASM2275121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022751215.1_ASM2275121v1_genomic.fna/checkm_input GCF_022751215.1_ASM2275121v1_genomic.fna/checkm_result [2024-01-24 13:11:16,029] [INFO] Task succeeded: CheckM [2024-01-24 13:11:16,031] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 16.67% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:11:16,057] [INFO] ===== Completeness check finished ===== [2024-01-24 13:11:16,058] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:11:16,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022751215.1_ASM2275121v1_genomic.fna/markers.fasta) [2024-01-24 13:11:16,059] [INFO] Task started: Blastn [2024-01-24 13:11:16,059] [INFO] Running command: blastn -query GCF_022751215.1_ASM2275121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ee1b1a6-743c-4114-a880-8ab839bbdb07/dqc_reference/reference_markers_gtdb.fasta -out GCF_022751215.1_ASM2275121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:11:18,104] [INFO] Task succeeded: Blastn [2024-01-24 13:11:18,108] [INFO] Selected 18 target genomes. [2024-01-24 13:11:18,108] [INFO] Target genome list was writen to GCF_022751215.1_ASM2275121v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:11:18,343] [INFO] Task started: fastANI [2024-01-24 13:11:18,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68cec90-db98-4736-aac0-5269c9e12731/GCF_022751215.1_ASM2275121v1_genomic.fna.gz --refList GCF_022751215.1_ASM2275121v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022751215.1_ASM2275121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:12:01,912] [INFO] Task succeeded: fastANI [2024-01-24 13:12:01,932] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 13:12:01,933] [INFO] GTDB search result -------------------------------------------------------------------------------- accession gtdb_species ani matched_fragments total_fragments gtdb_taxonomy ani_circumscription_radius mean_intra_species_ani min_intra_species_ani mean_intra_species_af min_intra_species_af num_clustered_genomes status GCF_009733595.1 s__Spirillospora litoris 93.0369 2499 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 99.22 99.22 0.97 0.97 2 - GCF_001552215.1 s__Spirillospora macra 85.6634 1936 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_004349215.1 s__Spirillospora rubrisoli 85.2055 1778 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_900659635.1 s__Spirillospora roseirufa 84.4811 1644 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_900659615.1 s__Spirillospora fibrosa 84.4328 1721 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_004348335.1 s__Spirillospora bangladeshensis 84.1083 1427 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_008327685.1 s__Spirillospora sp008327685 83.9614 1686 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_008923365.1 s__Spirillospora montaniterrae 83.9447 1694 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_013211575.1 s__Spirillospora verrucosospora 83.918 1806 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 95.82 95.82 0.89 0.89 2 - GCF_013364275.1 s__Spirillospora sp013364275 83.7827 1726 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_014208105.1 s__Spirillospora coerulea 83.7492 1689 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 100.00 100.00 1.00 1.00 2 - GCF_017573545.1 s__Spirillospora nitritigenes 83.7195 1779 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 95.12 95.12 0.83 0.83 2 - GCF_005889745.1 s__Spirillospora geliboluensis 83.6963 1444 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_004349235.1 s__Spirillospora darangshiensis 83.6288 1608 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_006547145.1 s__Spirillospora sp006547145 83.5817 1703 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_004348515.1 s__Spirillospora sp004348515 83.3604 1379 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_004348425.1 s__Spirillospora sp004348425 83.3023 1466 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 N/A N/A N/A N/A 1 - GCF_000425065.1 s__Spirillospora rifamycini 82.5657 1583 2978 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora 95.0 99.13 99.13 0.92 0.92 2 - -------------------------------------------------------------------------------- [2024-01-24 13:12:01,937] [INFO] GTDB search result was written to GCF_022751215.1_ASM2275121v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:12:01,938] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:12:01,942] [INFO] DFAST_QC result json was written to GCF_022751215.1_ASM2275121v1_genomic.fna/dqc_result.json [2024-01-24 13:12:01,942] [INFO] DFAST_QC completed! [2024-01-24 13:12:01,942] [INFO] Total running time: 0h3m4s