[2024-01-24 13:01:25,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:25,249] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:25,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference
[2024-01-24 13:01:26,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:26,710] [INFO] Task started: Prodigal
[2024-01-24 13:01:26,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg87fb99bc-ab3c-4fde-91d4-c8f38eb1760d/GCF_021474425.1_ASM2147442v1_genomic.fna.gz | prodigal -d GCF_021474425.1_ASM2147442v1_genomic.fna/cds.fna -a GCF_021474425.1_ASM2147442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:52,825] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:52,825] [INFO] Task started: HMMsearch
[2024-01-24 13:01:52,825] [INFO] Running command: hmmsearch --tblout GCF_021474425.1_ASM2147442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference/reference_markers.hmm GCF_021474425.1_ASM2147442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:53,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:53,255] [INFO] Found 6/6 markers.
[2024-01-24 13:01:53,347] [INFO] Query marker FASTA was written to GCF_021474425.1_ASM2147442v1_genomic.fna/markers.fasta
[2024-01-24 13:01:53,348] [INFO] Task started: Blastn
[2024-01-24 13:01:53,348] [INFO] Running command: blastn -query GCF_021474425.1_ASM2147442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference/reference_markers.fasta -out GCF_021474425.1_ASM2147442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:54,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:54,659] [INFO] Selected 18 target genomes.
[2024-01-24 13:01:54,659] [INFO] Target genome list was writen to GCF_021474425.1_ASM2147442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:54,665] [INFO] Task started: fastANI
[2024-01-24 13:01:54,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg87fb99bc-ab3c-4fde-91d4-c8f38eb1760d/GCF_021474425.1_ASM2147442v1_genomic.fna.gz --refList GCF_021474425.1_ASM2147442v1_genomic.fna/target_genomes.txt --output GCF_021474425.1_ASM2147442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:36,949] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:36,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:36,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:36,968] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:02:36,968] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:02:36,968] [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 caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	93.433	2287	2980	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	90.2997	2176	2980	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	89.7915	1978	2980	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	89.7185	2162	2980	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	89.6753	2203	2980	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	89.471	2222	2980	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	89.2681	2126	2980	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.4325	2004	2980	95	below_threshold
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	86.333	1930	2980	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.0192	1687	2980	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	85.9749	1859	2980	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	85.9708	1815	2980	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.9587	1792	2980	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.7892	1744	2980	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.6318	1704	2980	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.1795	1682	2980	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.5607	1665	2980	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	84.4814	1755	2980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:36,970] [INFO] DFAST Taxonomy check result was written to GCF_021474425.1_ASM2147442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:36,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:36,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:36,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference/checkm_data
[2024-01-24 13:02:36,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:37,070] [INFO] Task started: CheckM
[2024-01-24 13:02:37,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021474425.1_ASM2147442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021474425.1_ASM2147442v1_genomic.fna/checkm_input GCF_021474425.1_ASM2147442v1_genomic.fna/checkm_result
[2024-01-24 13:03:58,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:58,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:58,724] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:58,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:58,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021474425.1_ASM2147442v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:58,725] [INFO] Task started: Blastn
[2024-01-24 13:03:58,725] [INFO] Running command: blastn -query GCF_021474425.1_ASM2147442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg172d3868-12ad-4ac4-bc7b-8bce4fc6fb9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021474425.1_ASM2147442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:00,797] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:00,800] [INFO] Selected 15 target genomes.
[2024-01-24 13:04:00,801] [INFO] Target genome list was writen to GCF_021474425.1_ASM2147442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:00,811] [INFO] Task started: fastANI
[2024-01-24 13:04:00,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg87fb99bc-ab3c-4fde-91d4-c8f38eb1760d/GCF_021474425.1_ASM2147442v1_genomic.fna.gz --refList GCF_021474425.1_ASM2147442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021474425.1_ASM2147442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:38,179] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:38,195] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:04:38,195] [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_001514235.1	s__Streptomyces caeruleatus	93.4247	2289	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	93.3573	2229	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270495.1	s__Streptomyces viridochromogenes_A	91.6719	2214	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCF_004028635.1	s__Streptomyces cyaneus	90.3022	2175	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509475.1	s__Streptomyces regalis	89.9257	2169	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	89.7543	1983	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_015160855.1	s__Streptomyces ferrugineus	89.7352	2160	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	89.729	2119	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	89.6826	2203	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	89.6401	2202	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655715.1	s__Streptomyces lanatus	89.454	2224	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362785.1	s__Streptomyces sp013362785	89.2643	1616	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002027195.1	s__Streptomyces sp002027195	86.4985	1645	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_003955715.1	s__Streptomyces aquilus	86.3127	1934	2980	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	97.56	95.79	0.89	0.84	3	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	85.9774	1814	2980	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 13:04:38,197] [INFO] GTDB search result was written to GCF_021474425.1_ASM2147442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:38,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:38,201] [INFO] DFAST_QC result json was written to GCF_021474425.1_ASM2147442v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:38,201] [INFO] DFAST_QC completed!
[2024-01-24 13:04:38,201] [INFO] Total running time: 0h3m13s