[2024-01-25 18:59:50,733] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,735] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference
[2024-01-25 18:59:51,869] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,871] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ff20a2d-cdc1-4766-bd2d-004b7f73fdac/GCF_003074055.1_ASM307405v1_genomic.fna.gz | prodigal -d GCF_003074055.1_ASM307405v1_genomic.fna/cds.fna -a GCF_003074055.1_ASM307405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:11,069] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:11,070] [INFO] Task started: HMMsearch
[2024-01-25 19:00:11,070] [INFO] Running command: hmmsearch --tblout GCF_003074055.1_ASM307405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference/reference_markers.hmm GCF_003074055.1_ASM307405v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:11,375] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:11,376] [INFO] Found 6/6 markers.
[2024-01-25 19:00:11,434] [INFO] Query marker FASTA was written to GCF_003074055.1_ASM307405v1_genomic.fna/markers.fasta
[2024-01-25 19:00:11,434] [INFO] Task started: Blastn
[2024-01-25 19:00:11,434] [INFO] Running command: blastn -query GCF_003074055.1_ASM307405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference/reference_markers.fasta -out GCF_003074055.1_ASM307405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:12,697] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:12,700] [INFO] Selected 24 target genomes.
[2024-01-25 19:00:12,701] [INFO] Target genome list was writen to GCF_003074055.1_ASM307405v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:12,716] [INFO] Task started: fastANI
[2024-01-25 19:00:12,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff20a2d-cdc1-4766-bd2d-004b7f73fdac/GCF_003074055.1_ASM307405v1_genomic.fna.gz --refList GCF_003074055.1_ASM307405v1_genomic.fna/target_genomes.txt --output GCF_003074055.1_ASM307405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:02,063] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:02,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:02,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:02,077] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:02,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:02,078] [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 nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	100.0	2547	2547	95	conclusive
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	87.6339	2039	2547	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	87.5819	2037	2547	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	87.3887	1936	2547	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	87.2912	1662	2547	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	87.2573	1818	2547	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	87.1811	1923	2547	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	87.1332	1962	2547	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	87.0857	1975	2547	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.3279	1842	2547	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	85.3109	1680	2547	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	85.3073	1697	2547	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	85.2737	1663	2547	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2668	1669	2547	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.1923	1721	2547	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.1859	1696	2547	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.1772	1774	2547	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	85.1221	1334	2547	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	85.1142	1689	2547	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.0179	1387	2547	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.0107	1621	2547	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	84.9718	1612	2547	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	84.9626	1621	2547	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	84.8401	1613	2547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:02,079] [INFO] DFAST Taxonomy check result was written to GCF_003074055.1_ASM307405v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:02,080] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:02,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:02,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference/checkm_data
[2024-01-25 19:01:02,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:02,152] [INFO] Task started: CheckM
[2024-01-25 19:01:02,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003074055.1_ASM307405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003074055.1_ASM307405v1_genomic.fna/checkm_input GCF_003074055.1_ASM307405v1_genomic.fna/checkm_result
[2024-01-25 19:03:17,376] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:17,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:17,396] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:17,396] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:17,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003074055.1_ASM307405v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:17,397] [INFO] Task started: Blastn
[2024-01-25 19:03:17,397] [INFO] Running command: blastn -query GCF_003074055.1_ASM307405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdf36d33-1531-4c4f-a336-afd39a98c351/dqc_reference/reference_markers_gtdb.fasta -out GCF_003074055.1_ASM307405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:19,507] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:19,509] [INFO] Selected 18 target genomes.
[2024-01-25 19:03:19,509] [INFO] Target genome list was writen to GCF_003074055.1_ASM307405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:19,524] [INFO] Task started: fastANI
[2024-01-25 19:03:19,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff20a2d-cdc1-4766-bd2d-004b7f73fdac/GCF_003074055.1_ASM307405v1_genomic.fna.gz --refList GCF_003074055.1_ASM307405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003074055.1_ASM307405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:00,095] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:00,106] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:00,106] [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_003074055.1	s__Streptomyces nigra	100.0	2547	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	conclusive
GCF_001509795.1	s__Streptomyces sp001509795	93.0816	2189	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_008973465.1	s__Streptomyces sp008973465	93.0782	2221	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704715.1	s__Streptomyces chartreusis	87.661	2037	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	-
GCF_008042075.1	s__Streptomyces sp008042075	87.3914	1965	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	87.3856	1934	2547	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	87.2645	1817	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_000719285.1	s__Streptomyces bicolor	87.2229	1860	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001514235.1	s__Streptomyces caeruleatus	87.1534	1927	2547	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	87.1102	1967	2547	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	87.095	1868	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018604545.1	s__Streptomyces sp018604545	85.4773	1760	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	85.2146	1710	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665435.1	s__Streptomyces fungicidicus_A	85.2013	1679	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.42	0.93	0.90	4	-
GCA_014656175.1	s__Streptomyces werraensis	85.0052	1660	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649575.1	s__Streptomyces griseoincarnatus	84.9646	1670	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.24	97.52	0.91	0.85	21	-
GCF_014649835.1	s__Streptomyces pilosus	84.9522	1622	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.43	99.43	0.94	0.94	2	-
GCA_000715605.1	s__Streptomyces speibonae	84.7446	1669	2547	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.03	99.02	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:00,108] [INFO] GTDB search result was written to GCF_003074055.1_ASM307405v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:00,108] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:00,112] [INFO] DFAST_QC result json was written to GCF_003074055.1_ASM307405v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:00,112] [INFO] DFAST_QC completed!
[2024-01-25 19:04:00,112] [INFO] Total running time: 0h4m9s