[2024-01-24 14:55:25,691] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:25,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:25,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference
[2024-01-24 14:55:27,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:27,065] [INFO] Task started: Prodigal
[2024-01-24 14:55:27,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg68e1ba2e-a716-47fe-b93b-1257692b748b/GCF_003963535.1_ASM396353v1_genomic.fna.gz | prodigal -d GCF_003963535.1_ASM396353v1_genomic.fna/cds.fna -a GCF_003963535.1_ASM396353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:00,900] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:00,901] [INFO] Task started: HMMsearch
[2024-01-24 14:56:00,901] [INFO] Running command: hmmsearch --tblout GCF_003963535.1_ASM396353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference/reference_markers.hmm GCF_003963535.1_ASM396353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:01,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:01,269] [INFO] Found 6/6 markers.
[2024-01-24 14:56:01,346] [INFO] Query marker FASTA was written to GCF_003963535.1_ASM396353v1_genomic.fna/markers.fasta
[2024-01-24 14:56:01,347] [INFO] Task started: Blastn
[2024-01-24 14:56:01,347] [INFO] Running command: blastn -query GCF_003963535.1_ASM396353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference/reference_markers.fasta -out GCF_003963535.1_ASM396353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:02,675] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:02,679] [INFO] Selected 17 target genomes.
[2024-01-24 14:56:02,680] [INFO] Target genome list was writen to GCF_003963535.1_ASM396353v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:02,687] [INFO] Task started: fastANI
[2024-01-24 14:56:02,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e1ba2e-a716-47fe-b93b-1257692b748b/GCF_003963535.1_ASM396353v1_genomic.fna.gz --refList GCF_003963535.1_ASM396353v1_genomic.fna/target_genomes.txt --output GCF_003963535.1_ASM396353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:44,662] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:44,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:44,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:44,677] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:44,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:44,677] [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 cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	100.0	3537	3559	95	conclusive
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	90.6698	2495	3559	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	90.0354	2252	3559	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	89.7187	2406	3559	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	89.6524	2404	3559	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	89.2246	2475	3559	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	87.1391	2240	3559	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.3317	2224	3559	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.0736	1898	3559	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.83	2134	3559	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.5971	1934	3559	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.5358	2003	3559	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	84.629	1531	3559	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	84.4816	1936	3559	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	84.3931	2028	3559	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	84.3278	1993	3559	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	84.2286	1652	3559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:44,679] [INFO] DFAST Taxonomy check result was written to GCF_003963535.1_ASM396353v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:44,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:44,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:44,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference/checkm_data
[2024-01-24 14:56:44,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:44,773] [INFO] Task started: CheckM
[2024-01-24 14:56:44,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003963535.1_ASM396353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003963535.1_ASM396353v1_genomic.fna/checkm_input GCF_003963535.1_ASM396353v1_genomic.fna/checkm_result
[2024-01-24 14:59:15,264] [INFO] Task succeeded: CheckM
[2024-01-24 14:59:15,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:59:15,289] [INFO] ===== Completeness check finished =====
[2024-01-24 14:59:15,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:59:15,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003963535.1_ASM396353v1_genomic.fna/markers.fasta)
[2024-01-24 14:59:15,290] [INFO] Task started: Blastn
[2024-01-24 14:59:15,290] [INFO] Running command: blastn -query GCF_003963535.1_ASM396353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03c052e-e97a-4ae2-83a6-e7da1f9f2c95/dqc_reference/reference_markers_gtdb.fasta -out GCF_003963535.1_ASM396353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:59:17,357] [INFO] Task succeeded: Blastn
[2024-01-24 14:59:17,361] [INFO] Selected 14 target genomes.
[2024-01-24 14:59:17,361] [INFO] Target genome list was writen to GCF_003963535.1_ASM396353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:59:17,370] [INFO] Task started: fastANI
[2024-01-24 14:59:17,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e1ba2e-a716-47fe-b93b-1257692b748b/GCF_003963535.1_ASM396353v1_genomic.fna.gz --refList GCF_003963535.1_ASM396353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003963535.1_ASM396353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:59:55,465] [INFO] Task succeeded: fastANI
[2024-01-24 14:59:55,477] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:59:55,478] [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_003963535.1	s__Streptomyces cyaneochromogenes	100.0	3531	3559	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_900103585.1	s__Streptomyces sp900103585	92.2263	2728	3559	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	91.7387	2504	3559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004028635.1	s__Streptomyces cyaneus	90.7001	2490	3559	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	90.1556	2427	3559	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	90.0236	2253	3559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCA_013362785.1	s__Streptomyces sp013362785	89.9904	1839	3559	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	89.9859	2366	3559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCF_008042075.1	s__Streptomyces sp008042075	89.8298	2443	3559	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	89.6337	2407	3559	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	89.6328	2362	3559	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	89.3308	2469	3559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	-
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	84.8997	1899	3559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857135.1	s__Streptomyces sp009857135	84.2842	1795	3559	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 14:59:55,480] [INFO] GTDB search result was written to GCF_003963535.1_ASM396353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:59:55,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:59:55,484] [INFO] DFAST_QC result json was written to GCF_003963535.1_ASM396353v1_genomic.fna/dqc_result.json
[2024-01-24 14:59:55,485] [INFO] DFAST_QC completed!
[2024-01-24 14:59:55,485] [INFO] Total running time: 0h4m30s