[2024-01-24 13:01:49,727] [INFO] DFAST_QC pipeline started. [2024-01-24 13:01:49,729] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:01:49,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference [2024-01-24 13:01:51,033] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:01:51,035] [INFO] Task started: Prodigal [2024-01-24 13:01:51,035] [INFO] Running command: gunzip -c /var/lib/cwl/stgc727c6f5-e956-46db-9399-a095644c844d/GCF_000583875.1_ASM58387v1_genomic.fna.gz | prodigal -d GCF_000583875.1_ASM58387v1_genomic.fna/cds.fna -a GCF_000583875.1_ASM58387v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:01:53,139] [INFO] Task succeeded: Prodigal [2024-01-24 13:01:53,139] [INFO] Task started: HMMsearch [2024-01-24 13:01:53,140] [INFO] Running command: hmmsearch --tblout GCF_000583875.1_ASM58387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference/reference_markers.hmm GCF_000583875.1_ASM58387v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:01:53,359] [INFO] Task succeeded: HMMsearch [2024-01-24 13:01:53,363] [INFO] Found 6/6 markers. [2024-01-24 13:01:53,403] [INFO] Query marker FASTA was written to GCF_000583875.1_ASM58387v1_genomic.fna/markers.fasta [2024-01-24 13:01:53,403] [INFO] Task started: Blastn [2024-01-24 13:01:53,404] [INFO] Running command: blastn -query GCF_000583875.1_ASM58387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference/reference_markers.fasta -out GCF_000583875.1_ASM58387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:01:54,034] [INFO] Task succeeded: Blastn [2024-01-24 13:01:54,056] [INFO] Selected 12 target genomes. [2024-01-24 13:01:54,057] [INFO] Target genome list was writen to GCF_000583875.1_ASM58387v1_genomic.fna/target_genomes.txt [2024-01-24 13:01:54,108] [INFO] Task started: fastANI [2024-01-24 13:01:54,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgc727c6f5-e956-46db-9399-a095644c844d/GCF_000583875.1_ASM58387v1_genomic.fna.gz --refList GCF_000583875.1_ASM58387v1_genomic.fna/target_genomes.txt --output GCF_000583875.1_ASM58387v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:01:57,906] [INFO] Task succeeded: fastANI [2024-01-24 13:01:57,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:01:57,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:01:57,972] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:01:57,973] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:01:57,973] [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 Chlamydia avium strain=10DC88 GCA_000583875.1 1457141 1457141 type True 100.0 349 349 95 conclusive Chlamydia gallinacea strain=08-1274/3 GCA_000471025.2 1457153 1457153 type True 82.1787 282 349 95 below_threshold Chlamydia psittaci strain=6BC GCA_000191925.1 83554 83554 type True 78.6273 146 349 95 below_threshold Chlamydia psittaci strain=6BC GCA_000204255.1 83554 83554 type True 78.6004 146 349 95 below_threshold Chlamydia caviae GCA_000007605.1 83557 83557 type True 78.5593 154 349 95 below_threshold Chlamydia poikilotherma strain=S15-834K GCA_900239975.1 1967783 1967783 type True 78.4675 160 349 95 below_threshold Chlamydia buteonis GCA_900634605.1 2494525 2494525 type True 78.4182 154 349 95 below_threshold Chlamydia abortus strain=GIMC 2006:CabB577 GCA_002895085.1 83555 83555 type True 78.332 151 349 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:01:57,976] [INFO] DFAST Taxonomy check result was written to GCF_000583875.1_ASM58387v1_genomic.fna/tc_result.tsv [2024-01-24 13:01:57,977] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:01:57,977] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:01:57,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference/checkm_data [2024-01-24 13:01:57,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:01:58,004] [INFO] Task started: CheckM [2024-01-24 13:01:58,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000583875.1_ASM58387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000583875.1_ASM58387v1_genomic.fna/checkm_input GCF_000583875.1_ASM58387v1_genomic.fna/checkm_result [2024-01-24 13:02:15,658] [INFO] Task succeeded: CheckM [2024-01-24 13:02:15,659] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:02:15,679] [INFO] ===== Completeness check finished ===== [2024-01-24 13:02:15,680] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:02:15,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000583875.1_ASM58387v1_genomic.fna/markers.fasta) [2024-01-24 13:02:15,681] [INFO] Task started: Blastn [2024-01-24 13:02:15,681] [INFO] Running command: blastn -query GCF_000583875.1_ASM58387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7606976-60b0-4643-947b-e2268b069883/dqc_reference/reference_markers_gtdb.fasta -out GCF_000583875.1_ASM58387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:02:16,930] [INFO] Task succeeded: Blastn [2024-01-24 13:02:16,934] [INFO] Selected 16 target genomes. [2024-01-24 13:02:16,934] [INFO] Target genome list was writen to GCF_000583875.1_ASM58387v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:02:16,946] [INFO] Task started: fastANI [2024-01-24 13:02:16,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgc727c6f5-e956-46db-9399-a095644c844d/GCF_000583875.1_ASM58387v1_genomic.fna.gz --refList GCF_000583875.1_ASM58387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000583875.1_ASM58387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:02:21,824] [INFO] Task succeeded: fastANI [2024-01-24 13:02:21,871] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:02:21,871] [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_000583875.1 s__Chlamydophila avium 100.0 349 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.57 99.56 1.00 0.99 4 conclusive GCF_000471025.2 s__Chlamydophila gallinacea 82.1787 282 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.52 99.52 0.99 0.99 2 - GCF_000204255.1 s__Chlamydophila psittaci 78.6004 146 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.65 97.64 1.00 0.97 66 - GCF_000007605.1 s__Chlamydophila caviae 78.5593 154 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_900239975.1 s__Chlamydophila sp900239975 78.4675 160 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_900634605.1 s__Chlamydophila buteonis 78.4182 154 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.99 99.99 1.00 1.00 3 - GCF_018343815.1 s__Chlamydophila sp018343815 78.2518 170 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_000009945.1 s__Chlamydophila felis 78.1612 151 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_002817655.1 s__Chlamydophila corallus 77.5746 73 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_001653975.1 s__Chlamydophila sp001653975 77.0305 77 349 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:02:21,875] [INFO] GTDB search result was written to GCF_000583875.1_ASM58387v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:02:21,876] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:02:21,880] [INFO] DFAST_QC result json was written to GCF_000583875.1_ASM58387v1_genomic.fna/dqc_result.json [2024-01-24 13:02:21,881] [INFO] DFAST_QC completed! [2024-01-24 13:02:21,881] [INFO] Total running time: 0h0m32s