[2024-01-24 13:13:12,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,432] [INFO] DQC Reference Directory: /var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference
[2024-01-24 13:13:13,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,957] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3d6e066-0381-4176-894d-ef0b109ea56c/GCF_027270315.1_ASM2727031v1_genomic.fna.gz | prodigal -d GCF_027270315.1_ASM2727031v1_genomic.fna/cds.fna -a GCF_027270315.1_ASM2727031v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:43,426] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:43,427] [INFO] Task started: HMMsearch
[2024-01-24 13:13:43,427] [INFO] Running command: hmmsearch --tblout GCF_027270315.1_ASM2727031v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference/reference_markers.hmm GCF_027270315.1_ASM2727031v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:43,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:43,921] [INFO] Found 6/6 markers.
[2024-01-24 13:13:44,022] [INFO] Query marker FASTA was written to GCF_027270315.1_ASM2727031v1_genomic.fna/markers.fasta
[2024-01-24 13:13:44,023] [INFO] Task started: Blastn
[2024-01-24 13:13:44,024] [INFO] Running command: blastn -query GCF_027270315.1_ASM2727031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference/reference_markers.fasta -out GCF_027270315.1_ASM2727031v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:45,399] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:45,402] [INFO] Selected 27 target genomes.
[2024-01-24 13:13:45,403] [INFO] Target genome list was writen to GCF_027270315.1_ASM2727031v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:45,470] [INFO] Task started: fastANI
[2024-01-24 13:13:45,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3d6e066-0381-4176-894d-ef0b109ea56c/GCF_027270315.1_ASM2727031v1_genomic.fna.gz --refList GCF_027270315.1_ASM2727031v1_genomic.fna/target_genomes.txt --output GCF_027270315.1_ASM2727031v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:46,927] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:46,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:46,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:46,952] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:46,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:46,953] [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	94.4788	2538	3207	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	86.1743	2136	3207	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	86.1179	2120	3207	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	86.0602	2010	3207	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.0486	1931	3207	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.0088	2115	3207	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	86.0001	2071	3207	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.618	1891	3207	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.593	1781	3207	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.5897	1489	3207	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	85.4607	1937	3207	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.3946	1777	3207	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.3153	1860	3207	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2407	1800	3207	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.2104	1773	3207	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.1964	1739	3207	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	84.8344	1497	3207	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	84.8029	1895	3207	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	84.7165	1580	3207	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.7124	1665	3207	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	84.7106	1812	3207	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.5966	1798	3207	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	84.4771	1773	3207	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	84.443	1806	3207	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.3973	1789	3207	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	84.2702	1652	3207	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.0857	1752	3207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:46,955] [INFO] DFAST Taxonomy check result was written to GCF_027270315.1_ASM2727031v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:46,955] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:46,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:46,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference/checkm_data
[2024-01-24 13:14:46,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:47,039] [INFO] Task started: CheckM
[2024-01-24 13:14:47,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027270315.1_ASM2727031v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027270315.1_ASM2727031v1_genomic.fna/checkm_input GCF_027270315.1_ASM2727031v1_genomic.fna/checkm_result
[2024-01-24 13:16:52,147] [INFO] Task succeeded: CheckM
[2024-01-24 13:16:52,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:16:52,170] [INFO] ===== Completeness check finished =====
[2024-01-24 13:16:52,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:16:52,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027270315.1_ASM2727031v1_genomic.fna/markers.fasta)
[2024-01-24 13:16:52,171] [INFO] Task started: Blastn
[2024-01-24 13:16:52,171] [INFO] Running command: blastn -query GCF_027270315.1_ASM2727031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca3eaae8-eaaa-469f-a75f-1e34153bf4bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_027270315.1_ASM2727031v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:16:54,322] [INFO] Task succeeded: Blastn
[2024-01-24 13:16:54,329] [INFO] Selected 10 target genomes.
[2024-01-24 13:16:54,329] [INFO] Target genome list was writen to GCF_027270315.1_ASM2727031v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:16:54,341] [INFO] Task started: fastANI
[2024-01-24 13:16:54,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3d6e066-0381-4176-894d-ef0b109ea56c/GCF_027270315.1_ASM2727031v1_genomic.fna.gz --refList GCF_027270315.1_ASM2727031v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027270315.1_ASM2727031v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:20,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:20,164] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:20,164] [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
GCA_000715615.1	s__Streptomyces cinnabarinus	99.5919	3033	3207	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	94.482	2539	3207	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	90.2349	2236	3207	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	89.4452	2189	3207	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	87.7988	2062	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	86.1093	2079	3207	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	85.9336	2109	3207	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	85.1455	1958	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_004342105.1	s__Streptomyces sp004342105	84.418	1773	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489635.1	s__Streptomyces sp014489635	83.0974	1745	3207	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 13:17:20,165] [INFO] GTDB search result was written to GCF_027270315.1_ASM2727031v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:20,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:20,175] [INFO] DFAST_QC result json was written to GCF_027270315.1_ASM2727031v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:20,175] [INFO] DFAST_QC completed!
[2024-01-24 13:17:20,175] [INFO] Total running time: 0h4m8s