[2024-01-24 13:58:10,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference
[2024-01-24 13:58:11,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,802] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg547cb8d6-45d3-4dc7-b80c-ac65c33839d4/GCF_009709555.1_ASM970955v1_genomic.fna.gz | prodigal -d GCF_009709555.1_ASM970955v1_genomic.fna/cds.fna -a GCF_009709555.1_ASM970955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:35,408] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:35,408] [INFO] Task started: HMMsearch
[2024-01-24 13:58:35,408] [INFO] Running command: hmmsearch --tblout GCF_009709555.1_ASM970955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference/reference_markers.hmm GCF_009709555.1_ASM970955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:35,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:35,791] [INFO] Found 6/6 markers.
[2024-01-24 13:58:35,858] [INFO] Query marker FASTA was written to GCF_009709555.1_ASM970955v1_genomic.fna/markers.fasta
[2024-01-24 13:58:35,858] [INFO] Task started: Blastn
[2024-01-24 13:58:35,858] [INFO] Running command: blastn -query GCF_009709555.1_ASM970955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference/reference_markers.fasta -out GCF_009709555.1_ASM970955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,177] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:37,177] [INFO] Target genome list was writen to GCF_009709555.1_ASM970955v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:37,184] [INFO] Task started: fastANI
[2024-01-24 13:58:37,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg547cb8d6-45d3-4dc7-b80c-ac65c33839d4/GCF_009709555.1_ASM970955v1_genomic.fna.gz --refList GCF_009709555.1_ASM970955v1_genomic.fna/target_genomes.txt --output GCF_009709555.1_ASM970955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:24,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:24,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:24,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:24,157] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:24,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:24,157] [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 blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	100.0	2723	2731	95	conclusive
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.4765	1851	2731	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	86.4469	1793	2731	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	86.219	1887	2731	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	86.1497	1882	2731	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.9718	1848	2731	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.8819	1854	2731	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	85.8197	1835	2731	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.6438	1753	2731	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	85.6349	1752	2731	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2574	1614	2731	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	85.2484	1677	2731	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	85.1491	1655	2731	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.8674	1638	2731	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	84.8556	1509	2731	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	84.8436	1717	2731	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.8052	1649	2731	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.513	1345	2731	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	84.2359	1579	2731	95	below_threshold
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	84.004	1274	2731	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	83.8926	1665	2731	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	83.8829	1664	2731	95	below_threshold
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	83.8595	1644	2731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:24,161] [INFO] DFAST Taxonomy check result was written to GCF_009709555.1_ASM970955v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:24,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:24,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:24,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference/checkm_data
[2024-01-24 13:59:24,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:24,287] [INFO] Task started: CheckM
[2024-01-24 13:59:24,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009709555.1_ASM970955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009709555.1_ASM970955v1_genomic.fna/checkm_input GCF_009709555.1_ASM970955v1_genomic.fna/checkm_result
[2024-01-24 14:00:48,747] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:48,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:48,774] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:48,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:48,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009709555.1_ASM970955v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:48,776] [INFO] Task started: Blastn
[2024-01-24 14:00:48,776] [INFO] Running command: blastn -query GCF_009709555.1_ASM970955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96601208-f345-4f4d-8929-0489193ed4b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009709555.1_ASM970955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:50,971] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:50,975] [INFO] Selected 21 target genomes.
[2024-01-24 14:00:50,976] [INFO] Target genome list was writen to GCF_009709555.1_ASM970955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:51,004] [INFO] Task started: fastANI
[2024-01-24 14:00:51,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg547cb8d6-45d3-4dc7-b80c-ac65c33839d4/GCF_009709555.1_ASM970955v1_genomic.fna.gz --refList GCF_009709555.1_ASM970955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009709555.1_ASM970955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:36,612] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:36,636] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:36,636] [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_009709555.1	s__Streptomyces sp009709555	100.0	2721	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017948455.1	s__Streptomyces sp017948455	91.4164	1921	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948485.1	s__Streptomyces sp017948485	90.1078	1972	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291145.1	s__Streptomyces sp002291145	86.4784	1791	2731	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	86.4782	1786	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_001279775.1	s__Streptomyces sp001279775	86.3618	1850	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	86.2662	1848	2731	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	86.2069	1835	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015160855.1	s__Streptomyces ferrugineus	86.1948	1892	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	86.0709	1739	2731	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	85.9807	1846	2731	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	85.5184	1823	2731	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	85.3046	1746	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091315.1	s__Streptomyces sp900091315	85.2314	1634	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237655.1	s__Streptomyces sp002237655	85.1408	1685	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	84.9363	1605	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827595.1	s__Streptomyces sp007827595	84.5026	1683	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	84.2093	1544	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	84.0505	1449	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_005768555.2	s__Streptomyces sporangiiformans	83.9015	1662	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.8839	1625	2731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:36,637] [INFO] GTDB search result was written to GCF_009709555.1_ASM970955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:36,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:36,643] [INFO] DFAST_QC result json was written to GCF_009709555.1_ASM970955v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:36,643] [INFO] DFAST_QC completed!
[2024-01-24 14:01:36,643] [INFO] Total running time: 0h3m26s