[2024-01-24 11:26:39,052] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:39,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:39,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference
[2024-01-24 11:26:40,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,377] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,378] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2bb8e8b-585f-4126-9c1d-529d8f9f1037/GCF_023516615.1_ASM2351661v1_genomic.fna.gz | prodigal -d GCF_023516615.1_ASM2351661v1_genomic.fna/cds.fna -a GCF_023516615.1_ASM2351661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:05,116] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:05,117] [INFO] Task started: HMMsearch
[2024-01-24 11:27:05,117] [INFO] Running command: hmmsearch --tblout GCF_023516615.1_ASM2351661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference/reference_markers.hmm GCF_023516615.1_ASM2351661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:05,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:05,501] [INFO] Found 6/6 markers.
[2024-01-24 11:27:05,576] [INFO] Query marker FASTA was written to GCF_023516615.1_ASM2351661v1_genomic.fna/markers.fasta
[2024-01-24 11:27:05,576] [INFO] Task started: Blastn
[2024-01-24 11:27:05,577] [INFO] Running command: blastn -query GCF_023516615.1_ASM2351661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference/reference_markers.fasta -out GCF_023516615.1_ASM2351661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:06,847] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:06,850] [INFO] Selected 25 target genomes.
[2024-01-24 11:27:06,850] [INFO] Target genome list was writen to GCF_023516615.1_ASM2351661v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:06,865] [INFO] Task started: fastANI
[2024-01-24 11:27:06,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2bb8e8b-585f-4126-9c1d-529d8f9f1037/GCF_023516615.1_ASM2351661v1_genomic.fna.gz --refList GCF_023516615.1_ASM2351661v1_genomic.fna/target_genomes.txt --output GCF_023516615.1_ASM2351661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:28:03,857] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:03,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:28:03,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:28:03,882] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:28:03,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:28:03,882] [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 panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	100.0	2998	3016	95	conclusive
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	87.1322	1933	3016	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.0361	2089	3016	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	85.9099	1855	3016	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	85.9029	2104	3016	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	85.7794	1978	3016	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.7349	1893	3016	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.641	1917	3016	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	85.6176	2049	3016	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	85.3939	1945	3016	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.2515	1711	3016	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	85.2356	1816	3016	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	85.2328	1771	3016	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	85.171	1729	3016	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.1522	1578	3016	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	85.1247	1781	3016	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	85.0961	1930	3016	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	85.0878	2003	3016	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	85.0623	1777	3016	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.0178	1824	3016	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	84.8337	1844	3016	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.7831	1827	3016	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.7189	1423	3016	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	83.9862	1513	3016	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	83.9368	1504	3016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:28:03,884] [INFO] DFAST Taxonomy check result was written to GCF_023516615.1_ASM2351661v1_genomic.fna/tc_result.tsv
[2024-01-24 11:28:03,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:28:03,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:28:03,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference/checkm_data
[2024-01-24 11:28:03,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:28:03,974] [INFO] Task started: CheckM
[2024-01-24 11:28:03,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023516615.1_ASM2351661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023516615.1_ASM2351661v1_genomic.fna/checkm_input GCF_023516615.1_ASM2351661v1_genomic.fna/checkm_result
[2024-01-24 11:30:09,490] [INFO] Task succeeded: CheckM
[2024-01-24 11:30:09,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:30:09,520] [INFO] ===== Completeness check finished =====
[2024-01-24 11:30:09,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:30:09,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023516615.1_ASM2351661v1_genomic.fna/markers.fasta)
[2024-01-24 11:30:09,521] [INFO] Task started: Blastn
[2024-01-24 11:30:09,522] [INFO] Running command: blastn -query GCF_023516615.1_ASM2351661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47b88fe6-52db-4528-8b19-6a0589b2626c/dqc_reference/reference_markers_gtdb.fasta -out GCF_023516615.1_ASM2351661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:30:11,593] [INFO] Task succeeded: Blastn
[2024-01-24 11:30:11,597] [INFO] Selected 18 target genomes.
[2024-01-24 11:30:11,598] [INFO] Target genome list was writen to GCF_023516615.1_ASM2351661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:30:11,624] [INFO] Task started: fastANI
[2024-01-24 11:30:11,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2bb8e8b-585f-4126-9c1d-529d8f9f1037/GCF_023516615.1_ASM2351661v1_genomic.fna.gz --refList GCF_023516615.1_ASM2351661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023516615.1_ASM2351661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:30:54,221] [INFO] Task succeeded: fastANI
[2024-01-24 11:30:54,240] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:30:54,240] [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_001484565.1	s__Streptomyces sp001484565	97.4976	2733	3016	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_006715395.1	s__Streptomyces sp006715395	93.6569	2509	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_004343515.1	s__Streptomyces sp004343515	88.0622	2220	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_000720765.1	s__Streptomyces sp000720765	87.605	2154	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_003384795.1	s__Streptomyces sp003384795	87.3915	2085	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	87.3209	2121	3016	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	86.1337	2068	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	85.9237	2024	3016	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	85.8042	1973	3016	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	85.7436	1891	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	85.7076	1986	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCF_000719285.1	s__Streptomyces bicolor	85.6524	1887	3016	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	85.648	1916	3016	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	85.5573	1973	3016	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	85.3869	1947	3016	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	85.3162	1901	3016	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	84.0616	1667	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419765.1	s__Streptomyces torulosus	83.942	1520	3016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:30:54,242] [INFO] GTDB search result was written to GCF_023516615.1_ASM2351661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:30:54,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:30:54,248] [INFO] DFAST_QC result json was written to GCF_023516615.1_ASM2351661v1_genomic.fna/dqc_result.json
[2024-01-24 11:30:54,249] [INFO] DFAST_QC completed!
[2024-01-24 11:30:54,249] [INFO] Total running time: 0h4m15s