[2024-01-24 13:36:32,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference
[2024-01-24 13:36:33,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,588] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f32eec9-d804-422b-b624-978142378e14/GCF_000376565.1_ASM37656v1_genomic.fna.gz | prodigal -d GCF_000376565.1_ASM37656v1_genomic.fna/cds.fna -a GCF_000376565.1_ASM37656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:06,940] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:06,940] [INFO] Task started: HMMsearch
[2024-01-24 13:37:06,940] [INFO] Running command: hmmsearch --tblout GCF_000376565.1_ASM37656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference/reference_markers.hmm GCF_000376565.1_ASM37656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:07,396] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:07,398] [INFO] Found 6/6 markers.
[2024-01-24 13:37:07,491] [INFO] Query marker FASTA was written to GCF_000376565.1_ASM37656v1_genomic.fna/markers.fasta
[2024-01-24 13:37:07,492] [INFO] Task started: Blastn
[2024-01-24 13:37:07,492] [INFO] Running command: blastn -query GCF_000376565.1_ASM37656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference/reference_markers.fasta -out GCF_000376565.1_ASM37656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:08,718] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:08,721] [INFO] Selected 30 target genomes.
[2024-01-24 13:37:08,721] [INFO] Target genome list was writen to GCF_000376565.1_ASM37656v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:08,804] [INFO] Task started: fastANI
[2024-01-24 13:37:08,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f32eec9-d804-422b-b624-978142378e14/GCF_000376565.1_ASM37656v1_genomic.fna.gz --refList GCF_000376565.1_ASM37656v1_genomic.fna/target_genomes.txt --output GCF_000376565.1_ASM37656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:21,537] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:21,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:21,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:21,565] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:21,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:21,565] [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 hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	100.0	3852	3862	95	conclusive
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	91.297	2700	3862	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.5982	2239	3862	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.0945	1950	3862	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.9849	1999	3862	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	84.9183	2083	3862	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.9021	1814	3862	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.8333	2013	3862	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.6477	2143	3862	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.6098	2265	3862	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.5917	1906	3862	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	84.5305	2118	3862	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.4042	2009	3862	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	84.3562	1959	3862	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	84.3032	1972	3862	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	84.2989	1968	3862	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	83.9245	1634	3862	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	83.8613	1666	3862	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	83.7139	1839	3862	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	83.693	1835	3862	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	83.6668	1895	3862	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.5373	1981	3862	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	83.4959	1830	3862	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.4565	1978	3862	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	83.3826	1663	3862	95	below_threshold
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	83.2096	1851	3862	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.8597	1724	3862	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	80.9056	1224	3862	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	80.8736	1232	3862	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.0797	1051	3862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:21,567] [INFO] DFAST Taxonomy check result was written to GCF_000376565.1_ASM37656v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:21,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:21,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:21,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference/checkm_data
[2024-01-24 13:38:21,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:21,672] [INFO] Task started: CheckM
[2024-01-24 13:38:21,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376565.1_ASM37656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376565.1_ASM37656v1_genomic.fna/checkm_input GCF_000376565.1_ASM37656v1_genomic.fna/checkm_result
[2024-01-24 13:40:14,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:14,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:40:14,040] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:14,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:14,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376565.1_ASM37656v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:14,041] [INFO] Task started: Blastn
[2024-01-24 13:40:14,042] [INFO] Running command: blastn -query GCF_000376565.1_ASM37656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77aaa1ba-b7ff-4655-a276-b1ba799fb1e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376565.1_ASM37656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:16,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:16,058] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:16,058] [INFO] Target genome list was writen to GCF_000376565.1_ASM37656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:16,111] [INFO] Task started: fastANI
[2024-01-24 13:40:16,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f32eec9-d804-422b-b624-978142378e14/GCF_000376565.1_ASM37656v1_genomic.fna.gz --refList GCF_000376565.1_ASM37656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376565.1_ASM37656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:56,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:56,058] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:56,058] [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_000376565.1	s__Streptomyces hokutonensis	100.0	3852	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.37	96.37	0.82	0.82	2	conclusive
GCF_016654115.1	s__Streptomyces sp016654115	94.5175	2800	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.80	0.86	0.86	2	-
GCF_000716435.1	s__Streptomyces xylophagus	91.9199	2857	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612545.1	s__Streptomyces sp016612545	91.9166	2602	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716605.1	s__Streptomyces sp000716605	91.3039	2815	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367365.1	s__Streptomyces prunicolor	91.2878	2702	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016893485.2	s__Streptomyces sp016893485	90.4835	2608	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.92	98.82	0.96	0.95	4	-
GCF_000746395.1	s__Streptomyces mirabilis_A	87.9956	2456	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814935.1	s__Streptomyces sp003814935	86.6369	2494	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	83.8979	2205	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	83.6551	2079	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	83.383	1876	3862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	81.8662	1669	3862	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 13:40:56,060] [INFO] GTDB search result was written to GCF_000376565.1_ASM37656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:56,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:56,068] [INFO] DFAST_QC result json was written to GCF_000376565.1_ASM37656v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:56,068] [INFO] DFAST_QC completed!
[2024-01-24 13:40:56,068] [INFO] Total running time: 0h4m24s