[2024-01-24 12:45:10,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference
[2024-01-24 12:45:13,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,083] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg4887d7ef-5a6d-4338-bba0-36b04a606faa/GCF_014257025.1_ASM1425702v1_genomic.fna.gz | prodigal -d GCF_014257025.1_ASM1425702v1_genomic.fna/cds.fna -a GCF_014257025.1_ASM1425702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:39,188] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:39,188] [INFO] Task started: HMMsearch
[2024-01-24 12:45:39,189] [INFO] Running command: hmmsearch --tblout GCF_014257025.1_ASM1425702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference/reference_markers.hmm GCF_014257025.1_ASM1425702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:39,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:39,589] [INFO] Found 6/6 markers.
[2024-01-24 12:45:39,671] [INFO] Query marker FASTA was written to GCF_014257025.1_ASM1425702v1_genomic.fna/markers.fasta
[2024-01-24 12:45:39,671] [INFO] Task started: Blastn
[2024-01-24 12:45:39,672] [INFO] Running command: blastn -query GCF_014257025.1_ASM1425702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference/reference_markers.fasta -out GCF_014257025.1_ASM1425702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:41,001] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:41,008] [INFO] Selected 26 target genomes.
[2024-01-24 12:45:41,008] [INFO] Target genome list was writen to GCF_014257025.1_ASM1425702v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:41,039] [INFO] Task started: fastANI
[2024-01-24 12:45:41,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg4887d7ef-5a6d-4338-bba0-36b04a606faa/GCF_014257025.1_ASM1425702v1_genomic.fna.gz --refList GCF_014257025.1_ASM1425702v1_genomic.fna/target_genomes.txt --output GCF_014257025.1_ASM1425702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:37,590] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:37,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:37,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:37,614] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:46:37,614] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:46:37,615] [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 davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	90.5317	2188	3036	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.8564	2018	3036	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.6709	1998	3036	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	86.5505	2027	3036	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	86.5462	2043	3036	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.4697	2015	3036	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	86.3889	1997	3036	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	86.349	2025	3036	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	86.2801	1995	3036	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	86.2476	1999	3036	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	86.2188	1724	3036	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	86.1549	1881	3036	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	86.1125	1930	3036	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.0397	1860	3036	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.9555	1919	3036	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	85.9077	1655	3036	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.5865	1735	3036	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.5611	1785	3036	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.524	1442	3036	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	85.1485	1803	3036	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.0401	1534	3036	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	84.9782	1735	3036	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.8565	1613	3036	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	84.8197	1656	3036	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	84.4654	1807	3036	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	84.1382	1547	3036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:37,617] [INFO] DFAST Taxonomy check result was written to GCF_014257025.1_ASM1425702v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:37,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:37,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:37,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference/checkm_data
[2024-01-24 12:46:37,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:37,701] [INFO] Task started: CheckM
[2024-01-24 12:46:37,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014257025.1_ASM1425702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014257025.1_ASM1425702v1_genomic.fna/checkm_input GCF_014257025.1_ASM1425702v1_genomic.fna/checkm_result
[2024-01-24 12:48:02,363] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:02,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:02,387] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:02,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:02,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014257025.1_ASM1425702v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:02,388] [INFO] Task started: Blastn
[2024-01-24 12:48:02,388] [INFO] Running command: blastn -query GCF_014257025.1_ASM1425702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bafccbc-2d4a-474c-b462-f0e5a900f1ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_014257025.1_ASM1425702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:04,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:04,799] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:04,799] [INFO] Target genome list was writen to GCF_014257025.1_ASM1425702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:04,808] [INFO] Task started: fastANI
[2024-01-24 12:48:04,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg4887d7ef-5a6d-4338-bba0-36b04a606faa/GCF_014257025.1_ASM1425702v1_genomic.fna.gz --refList GCF_014257025.1_ASM1425702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014257025.1_ASM1425702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:34,990] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:35,005] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:35,006] [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_014257025.1	s__Streptomyces sp014257025	100.0	3029	3036	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_000349325.1	s__Streptomyces davaonensis	90.5394	2188	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715615.1	s__Streptomyces cinnabarinus	90.1867	2170	3036	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	88.6257	1962	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	88.3211	1980	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	86.8742	2015	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	86.5078	2050	3036	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	86.4368	1925	3036	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	86.2848	1995	3036	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	86.2756	1994	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709555.1	s__Streptomyces sp009709555	86.1906	1728	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	85.3165	1902	3036	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:35,008] [INFO] GTDB search result was written to GCF_014257025.1_ASM1425702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:35,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:35,015] [INFO] DFAST_QC result json was written to GCF_014257025.1_ASM1425702v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:35,016] [INFO] DFAST_QC completed!
[2024-01-24 12:48:35,016] [INFO] Total running time: 0h3m25s