[2024-01-24 10:48:09,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f4aac01-721f-4a32-a466-dd36646fd281/GCF_014650875.1_ASM1465087v1_genomic.fna.gz | prodigal -d GCF_014650875.1_ASM1465087v1_genomic.fna/cds.fna -a GCF_014650875.1_ASM1465087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:51,870] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:51,871] [INFO] Task started: HMMsearch
[2024-01-24 10:48:51,871] [INFO] Running command: hmmsearch --tblout GCF_014650875.1_ASM1465087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference/reference_markers.hmm GCF_014650875.1_ASM1465087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:52,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:52,279] [INFO] Found 6/6 markers.
[2024-01-24 10:48:52,347] [INFO] Query marker FASTA was written to GCF_014650875.1_ASM1465087v1_genomic.fna/markers.fasta
[2024-01-24 10:48:52,348] [INFO] Task started: Blastn
[2024-01-24 10:48:52,348] [INFO] Running command: blastn -query GCF_014650875.1_ASM1465087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference/reference_markers.fasta -out GCF_014650875.1_ASM1465087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:53,721] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:53,726] [INFO] Selected 27 target genomes.
[2024-01-24 10:48:53,727] [INFO] Target genome list was writen to GCF_014650875.1_ASM1465087v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:53,739] [INFO] Task started: fastANI
[2024-01-24 10:48:53,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f4aac01-721f-4a32-a466-dd36646fd281/GCF_014650875.1_ASM1465087v1_genomic.fna.gz --refList GCF_014650875.1_ASM1465087v1_genomic.fna/target_genomes.txt --output GCF_014650875.1_ASM1465087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:59,679] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:59,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:59,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:59,701] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:59,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:59,702] [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 minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	100.0	3036	3043	95	conclusive
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	84.6577	1849	3043	95	below_threshold
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	84.6166	1722	3043	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.2724	1723	3043	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.2325	1697	3043	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	84.2179	1641	3043	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.2113	1570	3043	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	84.1176	1687	3043	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.1078	1639	3043	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	84.0852	1592	3043	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.0715	1493	3043	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	83.9502	1605	3043	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	83.9049	1609	3043	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	83.8912	1675	3043	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	83.8715	1556	3043	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.829	1467	3043	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.7738	1845	3043	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	83.757	1717	3043	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	83.701	1601	3043	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	83.5561	1628	3043	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	83.5482	1630	3043	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	83.3466	1619	3043	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	83.3388	1630	3043	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.2914	1683	3043	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	82.6681	1592	3043	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	82.4668	1592	3043	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.3224	1617	3043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:59,703] [INFO] DFAST Taxonomy check result was written to GCF_014650875.1_ASM1465087v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:59,704] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:59,704] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:59,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference/checkm_data
[2024-01-24 10:49:59,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:59,796] [INFO] Task started: CheckM
[2024-01-24 10:49:59,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650875.1_ASM1465087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650875.1_ASM1465087v1_genomic.fna/checkm_input GCF_014650875.1_ASM1465087v1_genomic.fna/checkm_result
[2024-01-24 10:52:09,062] [INFO] Task succeeded: CheckM
[2024-01-24 10:52:09,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:52:09,095] [INFO] ===== Completeness check finished =====
[2024-01-24 10:52:09,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:52:09,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650875.1_ASM1465087v1_genomic.fna/markers.fasta)
[2024-01-24 10:52:09,096] [INFO] Task started: Blastn
[2024-01-24 10:52:09,096] [INFO] Running command: blastn -query GCF_014650875.1_ASM1465087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecc7187-dfc4-4240-86cd-222968b1b213/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650875.1_ASM1465087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:52:11,308] [INFO] Task succeeded: Blastn
[2024-01-24 10:52:11,313] [INFO] Selected 26 target genomes.
[2024-01-24 10:52:11,313] [INFO] Target genome list was writen to GCF_014650875.1_ASM1465087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:52:11,361] [INFO] Task started: fastANI
[2024-01-24 10:52:11,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f4aac01-721f-4a32-a466-dd36646fd281/GCF_014650875.1_ASM1465087v1_genomic.fna.gz --refList GCF_014650875.1_ASM1465087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650875.1_ASM1465087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:53:08,927] [INFO] Task succeeded: fastANI
[2024-01-24 10:53:08,954] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:53:08,954] [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_014650875.1	s__Streptomyces minutiscleroticus	100.0	3036	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	conclusive
GCF_014650915.1	s__Streptomyces poonensis	84.682	1712	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	84.613	1856	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369065.1	s__Streptomyces sp008369065	84.5514	1815	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	84.4033	1567	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	84.3647	1744	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300165.1	s__Streptomyces sp002300165	84.3099	1626	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.35	96.35	0.87	0.87	2	-
GCF_011193355.1	s__Streptomyces sp011193355	84.2623	1620	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002946835.1	s__Streptomyces dengpaensis	84.1888	1575	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014650575.1	s__Streptomyces naganishii	84.1102	1588	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	84.105	1688	3043	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	84.094	1741	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	83.9534	1601	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	83.9137	1671	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_002920535.1	s__Streptomyces sp002920535	83.9008	1575	3043	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	83.8938	1784	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645835.1	s__Streptomyces albiflavescens	83.8132	1707	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	83.6981	1601	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_016860525.1	s__Streptomyces rubradiris	83.5393	1631	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	83.497	1693	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647875.1	s__Streptomyces brasiliensis	83.3597	1626	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	83.3591	1616	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679425.1	s__Streptomyces incarnatus_A	83.0523	1475	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_004684775.1	s__Streptomyces sp004684775	82.7276	1379	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646335.1	s__Streptomyces lasiicapitis	82.4726	1589	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_009769735.1	s__Streptomyces sp009769735	82.3553	1586	3043	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 10:53:08,958] [INFO] GTDB search result was written to GCF_014650875.1_ASM1465087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:53:08,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:53:08,993] [INFO] DFAST_QC result json was written to GCF_014650875.1_ASM1465087v1_genomic.fna/dqc_result.json
[2024-01-24 10:53:08,993] [INFO] DFAST_QC completed!
[2024-01-24 10:53:08,994] [INFO] Total running time: 0h4m59s