[2024-01-24 12:22:14,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference
[2024-01-24 12:22:15,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,773] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgdac6b847-0248-4310-bba6-5eed22a47caf/GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/cds.fna -a GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:29,916] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:29,916] [INFO] Task started: HMMsearch
[2024-01-24 12:22:29,916] [INFO] Running command: hmmsearch --tblout GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference/reference_markers.hmm GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:30,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:30,301] [INFO] Found 6/6 markers.
[2024-01-24 12:22:30,345] [INFO] Query marker FASTA was written to GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:30,348] [INFO] Task started: Blastn
[2024-01-24 12:22:30,348] [INFO] Running command: blastn -query GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference/reference_markers.fasta -out GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:31,661] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:31,664] [INFO] Selected 13 target genomes.
[2024-01-24 12:22:31,664] [INFO] Target genome list was writen to GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:31,669] [INFO] Task started: fastANI
[2024-01-24 12:22:31,670] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac6b847-0248-4310-bba6-5eed22a47caf/GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna.gz --refList GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:47,572] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:47,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:47,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:47,592] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:47,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:47,593] [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
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	85.111	1072	1653	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	84.699	996	1653	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.0691	887	1653	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	83.0668	943	1653	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	83.0306	913	1653	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	82.9919	952	1653	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	82.6194	950	1653	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	82.6112	982	1653	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.5073	986	1653	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	82.405	978	1653	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	82.317	939	1653	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	82.2705	916	1653	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	82.171	983	1653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:47,595] [INFO] DFAST Taxonomy check result was written to GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:22:47,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:47,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:47,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference/checkm_data
[2024-01-24 12:22:47,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:47,659] [INFO] Task started: CheckM
[2024-01-24 12:22:47,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/checkm_input GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:23:57,080] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:57,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:57,108] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:57,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:57,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:23:57,109] [INFO] Task started: Blastn
[2024-01-24 12:23:57,109] [INFO] Running command: blastn -query GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4931713d-fbf0-4212-afe5-30f0e13b4e56/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:58,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:58,829] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:58,829] [INFO] Target genome list was writen to GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:58,857] [INFO] Task started: fastANI
[2024-01-24 12:23:58,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac6b847-0248-4310-bba6-5eed22a47caf/GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna.gz --refList GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:16,083] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:16,096] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:16,096] [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_900188025.1	s__Blastococcus sp900188025	100.0	1651	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006717095.1	s__Blastococcus colisei	85.1132	1072	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410015.1	s__Blastococcus sp013410015	84.7834	1050	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570425.1	s__Blastococcus sp004570425	84.7693	962	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230285.1	s__Blastococcus sp900230285	84.7257	973	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112815.1	s__Blastococcus sp900112815	84.5171	1014	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570345.1	s__Blastococcus sp004570345	83.728	908	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319185.1	s__Blastococcus sp003319185	83.4549	909	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	83.0664	943	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900102115.1	s__Blastococcus sp900102115	83.0449	867	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221005.1	s__Blastococcus aggregatus	83.0304	892	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620185.1	s__Blastococcus sp000620185	82.8824	932	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102425.1	s__Blastococcus sp900102425	82.8424	874	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222955.1	s__Blastococcus sp005222955	82.6309	782	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	82.2448	920	1653	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:16,098] [INFO] GTDB search result was written to GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:16,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:16,102] [INFO] DFAST_QC result json was written to GCF_900188025.1_IMG-taxon_2724679778_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:24:16,102] [INFO] DFAST_QC completed!
[2024-01-24 12:24:16,102] [INFO] Total running time: 0h2m2s