[2024-01-24 13:46:01,370] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,372] [INFO] DQC Reference Directory: /var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference
[2024-01-24 13:46:02,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,691] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg41ed415b-38d9-4dfa-a959-2bc7d99c5ef0/GCF_014650255.1_ASM1465025v1_genomic.fna.gz | prodigal -d GCF_014650255.1_ASM1465025v1_genomic.fna/cds.fna -a GCF_014650255.1_ASM1465025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:28,342] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:28,342] [INFO] Task started: HMMsearch
[2024-01-24 13:46:28,342] [INFO] Running command: hmmsearch --tblout GCF_014650255.1_ASM1465025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference/reference_markers.hmm GCF_014650255.1_ASM1465025v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:28,734] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:28,736] [INFO] Found 6/6 markers.
[2024-01-24 13:46:28,804] [INFO] Query marker FASTA was written to GCF_014650255.1_ASM1465025v1_genomic.fna/markers.fasta
[2024-01-24 13:46:28,804] [INFO] Task started: Blastn
[2024-01-24 13:46:28,805] [INFO] Running command: blastn -query GCF_014650255.1_ASM1465025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference/reference_markers.fasta -out GCF_014650255.1_ASM1465025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:30,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:30,055] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:30,055] [INFO] Target genome list was writen to GCF_014650255.1_ASM1465025v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:30,061] [INFO] Task started: fastANI
[2024-01-24 13:46:30,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg41ed415b-38d9-4dfa-a959-2bc7d99c5ef0/GCF_014650255.1_ASM1465025v1_genomic.fna.gz --refList GCF_014650255.1_ASM1465025v1_genomic.fna/target_genomes.txt --output GCF_014650255.1_ASM1465025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:56,067] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:56,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:56,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:56,083] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:46:56,084] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:46:56,084] [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 violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	100.0	3024	3027	95	inconclusive
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	99.9949	3017	3027	95	inconclusive
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	96.9889	2662	3027	95	inconclusive
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	95.7188	2630	3027	95	inconclusive
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	95.7178	2607	3027	95	inconclusive
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.3752	2255	3027	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.2988	1810	3027	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	90.0716	1912	3027	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.0304	1807	3027	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	83.7955	1897	3027	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	83.7449	1910	3027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:56,086] [INFO] DFAST Taxonomy check result was written to GCF_014650255.1_ASM1465025v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:56,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:56,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:56,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference/checkm_data
[2024-01-24 13:46:56,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:56,167] [INFO] Task started: CheckM
[2024-01-24 13:46:56,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650255.1_ASM1465025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650255.1_ASM1465025v1_genomic.fna/checkm_input GCF_014650255.1_ASM1465025v1_genomic.fna/checkm_result
[2024-01-24 13:48:57,787] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:57,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:57,821] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:57,821] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:57,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650255.1_ASM1465025v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:57,822] [INFO] Task started: Blastn
[2024-01-24 13:48:57,822] [INFO] Running command: blastn -query GCF_014650255.1_ASM1465025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga763f916-a642-450a-94b3-7305902d5eca/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650255.1_ASM1465025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:59,909] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:59,916] [INFO] Selected 25 target genomes.
[2024-01-24 13:48:59,916] [INFO] Target genome list was writen to GCF_014650255.1_ASM1465025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:00,034] [INFO] Task started: fastANI
[2024-01-24 13:49:00,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg41ed415b-38d9-4dfa-a959-2bc7d99c5ef0/GCF_014650255.1_ASM1465025v1_genomic.fna.gz --refList GCF_014650255.1_ASM1465025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650255.1_ASM1465025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:55,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,775] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:55,776] [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
GCA_000715635.1	s__Streptomyces violaceus	96.5213	2606	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.39	95.19	0.85	0.83	5	conclusive
GCF_018604545.1	s__Streptomyces sp018604545	94.1777	2444	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	91.5682	2428	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCA_000415505.1	s__Streptomyces afghaniensis	91.5415	2182	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	91.5331	2330	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_014651035.1	s__Streptomyces lomondensis	91.4014	2255	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150735.1	s__Streptomyces africanus	91.274	2094	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018195615.1	s__Streptomyces tuirus_A	91.1996	2239	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	91.1023	2299	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648995.1	s__Streptomyces massasporeus	90.9237	2307	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCA_000696115.1	s__Streptomyces olindensis	90.9204	2263	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205055.1	s__Streptomyces luteogriseus	90.6259	2273	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_007655005.1	s__Streptomyces tibetensis	90.3216	2268	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014651075.1	s__Streptomyces djakartensis	90.2559	2010	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	85.9658	2056	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	85.9306	2160	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_014648815.1	s__Streptomyces flaveolus	85.904	1732	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	85.8853	2036	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	85.7657	1819	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	85.5172	1714	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282115.1	s__Streptomyces sp001282115	85.4786	1707	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_002939385.1	s__Streptomyces sp002939385	85.4537	1691	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCA_013362785.1	s__Streptomyces sp013362785	85.3804	1559	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	84.8396	1677	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_005768555.2	s__Streptomyces sporangiiformans	83.7652	1906	3027	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,778] [INFO] GTDB search result was written to GCF_014650255.1_ASM1465025v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:55,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:55,783] [INFO] DFAST_QC result json was written to GCF_014650255.1_ASM1465025v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:55,783] [INFO] DFAST_QC completed!
[2024-01-24 13:49:55,783] [INFO] Total running time: 0h3m54s