[2024-01-24 13:27:31,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference
[2024-01-24 13:27:33,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,303] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg48133186-0b9f-4784-b10c-7dd46dd2084e/GCF_014651055.1_ASM1465105v1_genomic.fna.gz | prodigal -d GCF_014651055.1_ASM1465105v1_genomic.fna/cds.fna -a GCF_014651055.1_ASM1465105v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:58,297] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:58,297] [INFO] Task started: HMMsearch
[2024-01-24 13:27:58,297] [INFO] Running command: hmmsearch --tblout GCF_014651055.1_ASM1465105v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference/reference_markers.hmm GCF_014651055.1_ASM1465105v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:58,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:58,664] [INFO] Found 6/6 markers.
[2024-01-24 13:27:58,733] [INFO] Query marker FASTA was written to GCF_014651055.1_ASM1465105v1_genomic.fna/markers.fasta
[2024-01-24 13:27:58,733] [INFO] Task started: Blastn
[2024-01-24 13:27:58,733] [INFO] Running command: blastn -query GCF_014651055.1_ASM1465105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference/reference_markers.fasta -out GCF_014651055.1_ASM1465105v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:00,056] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:00,059] [INFO] Selected 25 target genomes.
[2024-01-24 13:28:00,060] [INFO] Target genome list was writen to GCF_014651055.1_ASM1465105v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:00,119] [INFO] Task started: fastANI
[2024-01-24 13:28:00,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg48133186-0b9f-4784-b10c-7dd46dd2084e/GCF_014651055.1_ASM1465105v1_genomic.fna.gz --refList GCF_014651055.1_ASM1465105v1_genomic.fna/target_genomes.txt --output GCF_014651055.1_ASM1465105v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:56,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:56,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:56,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:56,180] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:56,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:56,181] [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 fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	100.0	2912	2915	95	conclusive
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	86.6441	2128	2915	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	86.6026	1891	2915	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	86.2319	1666	2915	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	84.7392	1739	2915	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	84.724	1735	2915	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.4796	1787	2915	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.4376	1800	2915	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.3048	1862	2915	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.2524	1704	2915	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.1526	1901	2915	95	below_threshold
Streptomyces fagopyri	strain=QMT-28	GCA_009498275.1	2662397	2662397	type	True	84.1497	1816	2915	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	84.1152	1790	2915	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	84.1137	1943	2915	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	84.0793	1900	2915	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	84.0775	1777	2915	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	84.0497	1700	2915	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.3096	1874	2915	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.2906	1560	2915	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.2336	1806	2915	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.1395	1814	2915	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.0462	1625	2915	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	82.9101	1663	2915	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	82.5577	1418	2915	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	82.5205	1614	2915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:56,183] [INFO] DFAST Taxonomy check result was written to GCF_014651055.1_ASM1465105v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:56,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:56,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:56,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference/checkm_data
[2024-01-24 13:28:56,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:56,287] [INFO] Task started: CheckM
[2024-01-24 13:28:56,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651055.1_ASM1465105v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651055.1_ASM1465105v1_genomic.fna/checkm_input GCF_014651055.1_ASM1465105v1_genomic.fna/checkm_result
[2024-01-24 13:30:59,325] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:59,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:59,361] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:59,361] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:59,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651055.1_ASM1465105v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:59,362] [INFO] Task started: Blastn
[2024-01-24 13:30:59,362] [INFO] Running command: blastn -query GCF_014651055.1_ASM1465105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc04fa531-fec1-46dd-975f-c696c2ff4679/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651055.1_ASM1465105v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:01,410] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:01,416] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:01,416] [INFO] Target genome list was writen to GCF_014651055.1_ASM1465105v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:01,441] [INFO] Task started: fastANI
[2024-01-24 13:31:01,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg48133186-0b9f-4784-b10c-7dd46dd2084e/GCF_014651055.1_ASM1465105v1_genomic.fna.gz --refList GCF_014651055.1_ASM1465105v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651055.1_ASM1465105v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:48,535] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:48,556] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:48,557] [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_014651055.1	s__Streptomyces fructofermentans	100.0	2912	2915	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_008905045.1	s__Streptomyces albicerus	86.7418	2053	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	86.7146	1993	2915	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	86.6337	2122	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	86.6125	2128	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	86.6108	1891	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_008369065.1	s__Streptomyces sp008369065	86.2673	1906	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	86.2413	1665	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_014650955.1	s__Streptomyces tauricus	86.19	2069	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070025.1	s__Streptomyces sp018070025	86.1455	2123	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024195.1	s__Streptomyces dioscori	86.0935	2106	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650275.1	s__Streptomyces mirabilis	84.148	1904	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_012273535.1	s__Streptomyces sp002846625	84.1179	1922	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4492	97.43	96.23	0.83	0.78	4	-
GCF_002911015.1	s__Streptomyces populi	84.0966	1774	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_001514115.1	s__Streptomyces olivochromogenes	84.0857	1949	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	97.99	96.97	0.89	0.84	4	-
GCF_002078175.1	s__Streptomyces sp002078175	84.0429	1870	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.16	97.16	0.90	0.90	2	-
GCF_012273515.1	s__Streptomyces sp012273515	84.0211	1878	2915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112535.1	s__Streptomyces rishiriensis	82.9513	1656	2915	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 13:31:48,561] [INFO] GTDB search result was written to GCF_014651055.1_ASM1465105v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:48,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:48,571] [INFO] DFAST_QC result json was written to GCF_014651055.1_ASM1465105v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:48,571] [INFO] DFAST_QC completed!
[2024-01-24 13:31:48,572] [INFO] Total running time: 0h4m17s