[2024-01-24 12:13:28,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference
[2024-01-24 12:13:30,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,073] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg0903f758-e676-4dcf-b091-4fb1c849620e/GCF_021462825.1_ASM2146282v1_genomic.fna.gz | prodigal -d GCF_021462825.1_ASM2146282v1_genomic.fna/cds.fna -a GCF_021462825.1_ASM2146282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:52,816] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:52,816] [INFO] Task started: HMMsearch
[2024-01-24 12:13:52,816] [INFO] Running command: hmmsearch --tblout GCF_021462825.1_ASM2146282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference/reference_markers.hmm GCF_021462825.1_ASM2146282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:53,237] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:53,238] [INFO] Found 6/6 markers.
[2024-01-24 12:13:53,300] [INFO] Query marker FASTA was written to GCF_021462825.1_ASM2146282v1_genomic.fna/markers.fasta
[2024-01-24 12:13:53,300] [INFO] Task started: Blastn
[2024-01-24 12:13:53,301] [INFO] Running command: blastn -query GCF_021462825.1_ASM2146282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference/reference_markers.fasta -out GCF_021462825.1_ASM2146282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:54,728] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:54,733] [INFO] Selected 23 target genomes.
[2024-01-24 12:13:54,733] [INFO] Target genome list was writen to GCF_021462825.1_ASM2146282v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:54,742] [INFO] Task started: fastANI
[2024-01-24 12:13:54,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg0903f758-e676-4dcf-b091-4fb1c849620e/GCF_021462825.1_ASM2146282v1_genomic.fna.gz --refList GCF_021462825.1_ASM2146282v1_genomic.fna/target_genomes.txt --output GCF_021462825.1_ASM2146282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:38,801] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:38,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:38,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:38,819] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:38,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:38,819] [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 glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	100.0	2544	2551	95	conclusive
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	86.7576	1372	2551	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	86.0648	1538	2551	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	86.0528	1526	2551	95	below_threshold
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	85.9329	1547	2551	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	84.5599	1625	2551	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	84.5314	1599	2551	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	84.3831	1687	2551	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.3029	1563	2551	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	84.3029	1638	2551	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.3017	1571	2551	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.2969	1420	2551	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.2633	1566	2551	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.2459	1677	2551	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.2244	1664	2551	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	84.1652	1589	2551	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.119	1624	2551	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	84.0879	1565	2551	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	83.9922	1576	2551	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	83.944	1305	2551	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.9302	1629	2551	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	83.8401	1603	2551	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	83.7917	1550	2551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:38,821] [INFO] DFAST Taxonomy check result was written to GCF_021462825.1_ASM2146282v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:38,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:38,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:38,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference/checkm_data
[2024-01-24 12:14:38,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:38,894] [INFO] Task started: CheckM
[2024-01-24 12:14:38,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021462825.1_ASM2146282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021462825.1_ASM2146282v1_genomic.fna/checkm_input GCF_021462825.1_ASM2146282v1_genomic.fna/checkm_result
[2024-01-24 12:16:24,806] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:24,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:24,842] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:24,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:24,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021462825.1_ASM2146282v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:24,844] [INFO] Task started: Blastn
[2024-01-24 12:16:24,844] [INFO] Running command: blastn -query GCF_021462825.1_ASM2146282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ae23f8-1c70-4fa3-a2b2-dc520d536d8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021462825.1_ASM2146282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:26,909] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:26,915] [INFO] Selected 19 target genomes.
[2024-01-24 12:16:26,915] [INFO] Target genome list was writen to GCF_021462825.1_ASM2146282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:26,930] [INFO] Task started: fastANI
[2024-01-24 12:16:26,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg0903f758-e676-4dcf-b091-4fb1c849620e/GCF_021462825.1_ASM2146282v1_genomic.fna.gz --refList GCF_021462825.1_ASM2146282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021462825.1_ASM2146282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:03,434] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:03,452] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:03,452] [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_001417775.1	s__Streptomyces sp001417775	87.9439	1804	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905555.1	s__Streptomyces sp014905555	87.2864	1819	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920635.1	s__Streptomyces sp002920635	87.0941	1683	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866645.1	s__Streptomyces colonosanans	86.7863	1368	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507435.1	s__Streptomyces sp001507435	86.4894	1777	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
GCF_008704995.1	s__Streptomyces nodosus	86.0645	1538	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	97.72	0.96	0.87	5	-
GCF_014650655.1	s__Streptomyces anandii	84.5685	1622	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	84.5153	1601	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715785.1	s__Streptomyces puniciscabiei	84.3963	1685	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.70	95.42	0.91	0.82	3	-
GCF_013046785.1	s__Streptomyces sp013046785	84.2941	1583	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	84.2613	1619	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	84.2563	1571	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_001735805.1	s__Streptomyces fodineus	84.25	1677	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484565.1	s__Streptomyces sp001484565	84.2359	1695	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.2061	1599	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	84.1388	1645	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_012273515.1	s__Streptomyces sp012273515	84.0096	1670	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009865385.1	s__Streptomyces sp009865385	83.8143	1434	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	83.8047	1547	2551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:03,454] [INFO] GTDB search result was written to GCF_021462825.1_ASM2146282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:03,455] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:03,459] [INFO] DFAST_QC result json was written to GCF_021462825.1_ASM2146282v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:03,459] [INFO] DFAST_QC completed!
[2024-01-24 12:17:03,459] [INFO] Total running time: 0h3m35s