[2024-01-24 13:46:01,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference
[2024-01-24 13:46:02,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,384] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,385] [INFO] Running command: gunzip -c /var/lib/cwl/stgde84f833-aa61-478a-8bfe-a0d20ba1cb3f/GCF_000696595.1_StrepLeeu1.0_genomic.fna.gz | prodigal -d GCF_000696595.1_StrepLeeu1.0_genomic.fna/cds.fna -a GCF_000696595.1_StrepLeeu1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:23,040] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:23,040] [INFO] Task started: HMMsearch
[2024-01-24 13:46:23,040] [INFO] Running command: hmmsearch --tblout GCF_000696595.1_StrepLeeu1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference/reference_markers.hmm GCF_000696595.1_StrepLeeu1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:23,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:23,417] [INFO] Found 6/6 markers.
[2024-01-24 13:46:23,482] [INFO] Query marker FASTA was written to GCF_000696595.1_StrepLeeu1.0_genomic.fna/markers.fasta
[2024-01-24 13:46:23,483] [INFO] Task started: Blastn
[2024-01-24 13:46:23,483] [INFO] Running command: blastn -query GCF_000696595.1_StrepLeeu1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference/reference_markers.fasta -out GCF_000696595.1_StrepLeeu1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:24,868] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:24,871] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:24,872] [INFO] Target genome list was writen to GCF_000696595.1_StrepLeeu1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:46:24,878] [INFO] Task started: fastANI
[2024-01-24 13:46:24,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgde84f833-aa61-478a-8bfe-a0d20ba1cb3f/GCF_000696595.1_StrepLeeu1.0_genomic.fna.gz --refList GCF_000696595.1_StrepLeeu1.0_genomic.fna/target_genomes.txt --output GCF_000696595.1_StrepLeeu1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:03,488] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:03,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:03,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:03,511] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:03,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:03,511] [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 leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	100.0	2318	2341	95	conclusive
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	99.9858	2340	2341	95	conclusive
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	94.7022	1738	2341	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.3354	1628	2341	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	87.2791	1576	2341	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	87.0351	1545	2341	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	86.6051	1595	2341	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.1003	1555	2341	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	86.0984	1262	2341	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	86.0973	1570	2341	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	86.0958	1568	2341	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.5654	1553	2341	95	below_threshold
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	85.5531	1542	2341	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.4358	1338	2341	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.1351	1341	2341	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.0952	1547	2341	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.8998	1378	2341	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	84.4197	1443	2341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,513] [INFO] DFAST Taxonomy check result was written to GCF_000696595.1_StrepLeeu1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:47:03,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:03,514] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:03,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference/checkm_data
[2024-01-24 13:47:03,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:03,592] [INFO] Task started: CheckM
[2024-01-24 13:47:03,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000696595.1_StrepLeeu1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000696595.1_StrepLeeu1.0_genomic.fna/checkm_input GCF_000696595.1_StrepLeeu1.0_genomic.fna/checkm_result
[2024-01-24 13:48:07,417] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:07,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:07,440] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:07,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:07,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000696595.1_StrepLeeu1.0_genomic.fna/markers.fasta)
[2024-01-24 13:48:07,441] [INFO] Task started: Blastn
[2024-01-24 13:48:07,441] [INFO] Running command: blastn -query GCF_000696595.1_StrepLeeu1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2233a793-0133-45cd-a5cf-9b5cfcc3cd25/dqc_reference/reference_markers_gtdb.fasta -out GCF_000696595.1_StrepLeeu1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:09,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:09,622] [INFO] Selected 21 target genomes.
[2024-01-24 13:48:09,622] [INFO] Target genome list was writen to GCF_000696595.1_StrepLeeu1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:09,642] [INFO] Task started: fastANI
[2024-01-24 13:48:09,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgde84f833-aa61-478a-8bfe-a0d20ba1cb3f/GCF_000696595.1_StrepLeeu1.0_genomic.fna.gz --refList GCF_000696595.1_StrepLeeu1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000696595.1_StrepLeeu1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:56,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:56,194] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:56,195] [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_001013905.1	s__Streptomyces leeuwenhoekii	99.9858	2340	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	99.67	99.36	0.97	0.94	3	conclusive
GCF_000931445.1	s__Streptomyces cyaneogriseus	96.49	1967	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	87.3313	1628	2341	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	87.2684	1577	2341	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	86.7886	1505	2341	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	86.6388	1591	2341	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	86.4238	1587	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	86.1196	1568	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_001905845.1	s__Streptomyces sp001905845	85.8192	1576	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018604545.1	s__Streptomyces sp018604545	85.7138	1498	2341	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	85.5766	1551	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_000158955.1	s__Streptomyces viridochromogenes_B	85.5083	1519	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715635.1	s__Streptomyces violaceus	85.5032	1538	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.39	95.19	0.85	0.83	5	-
GCF_002920535.1	s__Streptomyces sp002920535	85.4774	1478	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	85.1104	1545	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851625.1	s__Streptomyces sp003851625	85.1029	1569	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.0501	1531	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	85.0355	1432	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_014257025.1	s__Streptomyces sp014257025	84.9858	1471	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	84.7051	1503	2341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_014203595.1	s__Streptomyces echinatus	84.5528	1471	2341	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 13:48:56,196] [INFO] GTDB search result was written to GCF_000696595.1_StrepLeeu1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:56,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:56,204] [INFO] DFAST_QC result json was written to GCF_000696595.1_StrepLeeu1.0_genomic.fna/dqc_result.json
[2024-01-24 13:48:56,204] [INFO] DFAST_QC completed!
[2024-01-24 13:48:56,204] [INFO] Total running time: 0h2m55s