[2024-01-24 13:26:26,092] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,096] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference
[2024-01-24 13:26:27,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,286] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,286] [INFO] Running command: gunzip -c /var/lib/cwl/stg87a656cc-0618-4f30-8a02-f01e6b53b54a/GCF_024761905.1_ASM2476190v1_genomic.fna.gz | prodigal -d GCF_024761905.1_ASM2476190v1_genomic.fna/cds.fna -a GCF_024761905.1_ASM2476190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:45,283] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:45,284] [INFO] Task started: HMMsearch
[2024-01-24 13:26:45,285] [INFO] Running command: hmmsearch --tblout GCF_024761905.1_ASM2476190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference/reference_markers.hmm GCF_024761905.1_ASM2476190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:45,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:45,652] [INFO] Found 6/6 markers.
[2024-01-24 13:26:45,713] [INFO] Query marker FASTA was written to GCF_024761905.1_ASM2476190v1_genomic.fna/markers.fasta
[2024-01-24 13:26:45,714] [INFO] Task started: Blastn
[2024-01-24 13:26:45,714] [INFO] Running command: blastn -query GCF_024761905.1_ASM2476190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference/reference_markers.fasta -out GCF_024761905.1_ASM2476190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:47,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:47,114] [INFO] Selected 21 target genomes.
[2024-01-24 13:26:47,114] [INFO] Target genome list was writen to GCF_024761905.1_ASM2476190v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:47,294] [INFO] Task started: fastANI
[2024-01-24 13:26:47,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg87a656cc-0618-4f30-8a02-f01e6b53b54a/GCF_024761905.1_ASM2476190v1_genomic.fna.gz --refList GCF_024761905.1_ASM2476190v1_genomic.fna/target_genomes.txt --output GCF_024761905.1_ASM2476190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:19,228] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:19,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:19,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:19,280] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:27:19,280] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:27:19,281] [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
Streptomyces xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	88.9099	1562	1935	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.5105	1042	1935	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.4617	967	1935	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	81.3744	989	1935	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	81.0828	1132	1935	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	81.0795	1085	1935	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	81.0384	1081	1935	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	80.9103	1085	1935	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	80.8208	1103	1935	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	80.7896	900	1935	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.4734	957	1935	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	80.3209	935	1935	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.2704	841	1935	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.926	1004	1935	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	79.8625	874	1935	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.7059	795	1935	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	79.6363	799	1935	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	79.6302	924	1935	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	79.4109	870	1935	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	79.3078	917	1935	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	79.2848	892	1935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:19,283] [INFO] DFAST Taxonomy check result was written to GCF_024761905.1_ASM2476190v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:19,284] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:19,284] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:19,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference/checkm_data
[2024-01-24 13:27:19,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:19,345] [INFO] Task started: CheckM
[2024-01-24 13:27:19,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024761905.1_ASM2476190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024761905.1_ASM2476190v1_genomic.fna/checkm_input GCF_024761905.1_ASM2476190v1_genomic.fna/checkm_result
[2024-01-24 13:28:46,202] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:46,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,228] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:46,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:46,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024761905.1_ASM2476190v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:46,229] [INFO] Task started: Blastn
[2024-01-24 13:28:46,230] [INFO] Running command: blastn -query GCF_024761905.1_ASM2476190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f62848d-fadc-4fe7-a65e-2ad6ac8655ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_024761905.1_ASM2476190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:48,484] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:48,488] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:48,489] [INFO] Target genome list was writen to GCF_024761905.1_ASM2476190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:48,652] [INFO] Task started: fastANI
[2024-01-24 13:28:48,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg87a656cc-0618-4f30-8a02-f01e6b53b54a/GCF_024761905.1_ASM2476190v1_genomic.fna.gz --refList GCF_024761905.1_ASM2476190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024761905.1_ASM2476190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:16,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:16,798] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:16,799] [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_900116145.1	s__Streptomyces harbinensis	99.2661	1863	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	conclusive
GCF_000993785.3	s__Streptomyces xiamenensis	88.9224	1561	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	97.97	0.94	0.91	3	-
GCF_004348315.1	s__Streptomyces sp004348315	81.5809	1031	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	81.5067	1043	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.4677	966	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696235.1	s__Streptomyces triticirhizae	81.4138	984	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_001984575.1	s__Streptomyces sp001984575	80.9955	1141	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	80.9929	1088	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335015.1	s__Streptomyces sedi	80.9089	1085	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	80.8636	1071	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626535.1	s__Streptomyces hoynatensis	80.8459	1098	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004305975.1	s__Streptomyces otsuchiensis	80.792	900	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_000974485.1	s__Streptomyces sp000974485	80.6393	1078	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	80.2953	940	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	79.3357	907	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCA_003725745.1	s__Streptomyces sp003725745	79.3066	839	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097515.1	s__Streptomyces tirandamycinicus	79.2863	891	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	98.27	0.90	0.88	6	-
GCF_003999195.1	s__Streptomyces sp003999195	79.2056	829	1935	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:16,800] [INFO] GTDB search result was written to GCF_024761905.1_ASM2476190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:16,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:16,805] [INFO] DFAST_QC result json was written to GCF_024761905.1_ASM2476190v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:16,805] [INFO] DFAST_QC completed!
[2024-01-24 13:29:16,805] [INFO] Total running time: 0h2m51s