[2024-01-25 18:45:20,703] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:20,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:20,704] [INFO] DQC Reference Directory: /var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference
[2024-01-25 18:45:21,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:21,861] [INFO] Task started: Prodigal
[2024-01-25 18:45:21,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d3baee0-4245-4117-b9ab-79026b2ba9c8/GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/cds.fna -a GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:31,821] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:31,821] [INFO] Task started: HMMsearch
[2024-01-25 18:45:31,821] [INFO] Running command: hmmsearch --tblout GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference/reference_markers.hmm GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:32,032] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:32,034] [INFO] Found 6/6 markers.
[2024-01-25 18:45:32,070] [INFO] Query marker FASTA was written to GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:45:32,070] [INFO] Task started: Blastn
[2024-01-25 18:45:32,070] [INFO] Running command: blastn -query GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference/reference_markers.fasta -out GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:33,269] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:33,274] [INFO] Selected 17 target genomes.
[2024-01-25 18:45:33,275] [INFO] Target genome list was writen to GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:45:33,286] [INFO] Task started: fastANI
[2024-01-25 18:45:33,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d3baee0-4245-4117-b9ab-79026b2ba9c8/GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna.gz --refList GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:53,405] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:53,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:53,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:53,417] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:53,417] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:53,418] [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 aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	87.5103	1059	1378	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	83.7953	944	1378	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	83.7567	908	1378	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	83.6585	934	1378	95	below_threshold
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	83.6315	814	1378	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	83.5379	930	1378	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	83.2217	921	1378	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	82.7464	901	1378	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	82.722	867	1378	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	82.6938	880	1378	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	82.6784	897	1378	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	82.6485	889	1378	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	82.5956	896	1378	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.5944	906	1378	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	82.5717	871	1378	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	81.6734	793	1378	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	81.6076	775	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:53,419] [INFO] DFAST Taxonomy check result was written to GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:45:53,420] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:53,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:53,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference/checkm_data
[2024-01-25 18:45:53,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:53,462] [INFO] Task started: CheckM
[2024-01-25 18:45:53,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/checkm_input GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:46:53,037] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:53,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:53,058] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:53,058] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:53,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:46:53,059] [INFO] Task started: Blastn
[2024-01-25 18:46:53,059] [INFO] Running command: blastn -query GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge44e6790-57b1-477b-ab0c-731fdf6e3066/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:54,914] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:54,920] [INFO] Selected 13 target genomes.
[2024-01-25 18:46:54,920] [INFO] Target genome list was writen to GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:54,948] [INFO] Task started: fastANI
[2024-01-25 18:46:54,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d3baee0-4245-4117-b9ab-79026b2ba9c8/GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna.gz --refList GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:10,106] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:10,114] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:10,115] [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_900102425.1	s__Blastococcus sp900102425	100.0	1376	1378	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_003319105.1	s__Blastococcus sp003319105	89.923	1084	1378	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	87.8426	1078	1378	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	87.5179	1058	1378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612865.1	s__Blastococcus sp016612865	87.2735	1032	1378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000582785.1	s__Blastococcus massiliensis	85.9488	1022	1378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005222955.1	s__Blastococcus sp005222955	85.004	900	1378	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	84.9436	946	1378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682065.1	s__Blastococcus saxobsidens_B	83.9312	870	1378	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	83.6288	950	1378	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	83.5649	938	1378	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	83.4258	943	1378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188025.1	s__Blastococcus sp900188025	82.7645	876	1378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:10,116] [INFO] GTDB search result was written to GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:10,116] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:10,121] [INFO] DFAST_QC result json was written to GCF_900102425.1_IMG-taxon_2599185358_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:47:10,122] [INFO] DFAST_QC completed!
[2024-01-25 18:47:10,122] [INFO] Total running time: 0h1m49s