[2024-01-24 15:18:50,641] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:50,643] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:50,643] [INFO] DQC Reference Directory: /var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference
[2024-01-24 15:18:52,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,027] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dd52979-0e87-43ea-a068-86a684a51d53/GCF_014647875.1_ASM1464787v1_genomic.fna.gz | prodigal -d GCF_014647875.1_ASM1464787v1_genomic.fna/cds.fna -a GCF_014647875.1_ASM1464787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:25,194] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:25,194] [INFO] Task started: HMMsearch
[2024-01-24 15:19:25,194] [INFO] Running command: hmmsearch --tblout GCF_014647875.1_ASM1464787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference/reference_markers.hmm GCF_014647875.1_ASM1464787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:25,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:25,612] [INFO] Found 6/6 markers.
[2024-01-24 15:19:25,694] [INFO] Query marker FASTA was written to GCF_014647875.1_ASM1464787v1_genomic.fna/markers.fasta
[2024-01-24 15:19:25,694] [INFO] Task started: Blastn
[2024-01-24 15:19:25,695] [INFO] Running command: blastn -query GCF_014647875.1_ASM1464787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference/reference_markers.fasta -out GCF_014647875.1_ASM1464787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:27,012] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:27,015] [INFO] Selected 28 target genomes.
[2024-01-24 15:19:27,016] [INFO] Target genome list was writen to GCF_014647875.1_ASM1464787v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:27,036] [INFO] Task started: fastANI
[2024-01-24 15:19:27,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd52979-0e87-43ea-a068-86a684a51d53/GCF_014647875.1_ASM1464787v1_genomic.fna.gz --refList GCF_014647875.1_ASM1464787v1_genomic.fna/target_genomes.txt --output GCF_014647875.1_ASM1464787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:24,971] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:24,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:24,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:24,992] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:24,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:24,992] [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 brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	100.0	3427	3439	95	conclusive
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	86.0975	1864	3439	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	85.6847	1919	3439	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	85.4149	1804	3439	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	85.3993	1902	3439	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	85.3872	1803	3439	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	85.3379	1833	3439	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	85.3308	1794	3439	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.2938	1462	3439	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.2798	1815	3439	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	85.1512	1635	3439	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	85.1306	1827	3439	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	85.0753	1834	3439	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	85.0747	1939	3439	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.0507	1779	3439	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.0408	1837	3439	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.023	1739	3439	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	85.01	1737	3439	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.9577	1735	3439	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	84.9352	1689	3439	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.8579	1658	3439	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	84.7998	1718	3439	95	below_threshold
Streptomyces mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	84.7178	1774	3439	95	below_threshold
Streptomyces murinus	strain=NRRL B-2286	GCA_002154555.1	33900	33900	type	True	84.6681	1334	3439	95	below_threshold
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	84.0981	1454	3439	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	83.4044	1588	3439	95	below_threshold
Streptomyces nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	83.3614	1582	3439	95	below_threshold
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	83.3358	1602	3439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:24,998] [INFO] DFAST Taxonomy check result was written to GCF_014647875.1_ASM1464787v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:24,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:24,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:24,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference/checkm_data
[2024-01-24 15:20:25,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:25,105] [INFO] Task started: CheckM
[2024-01-24 15:20:25,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647875.1_ASM1464787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647875.1_ASM1464787v1_genomic.fna/checkm_input GCF_014647875.1_ASM1464787v1_genomic.fna/checkm_result
[2024-01-24 15:22:49,732] [INFO] Task succeeded: CheckM
[2024-01-24 15:22:49,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 15:22:49,764] [INFO] ===== Completeness check finished =====
[2024-01-24 15:22:49,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:22:49,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647875.1_ASM1464787v1_genomic.fna/markers.fasta)
[2024-01-24 15:22:49,765] [INFO] Task started: Blastn
[2024-01-24 15:22:49,765] [INFO] Running command: blastn -query GCF_014647875.1_ASM1464787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge14ad66a-6531-4654-8f09-bef70dd8080b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647875.1_ASM1464787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:22:51,918] [INFO] Task succeeded: Blastn
[2024-01-24 15:22:51,923] [INFO] Selected 29 target genomes.
[2024-01-24 15:22:51,924] [INFO] Target genome list was writen to GCF_014647875.1_ASM1464787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:22:52,017] [INFO] Task started: fastANI
[2024-01-24 15:22:52,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd52979-0e87-43ea-a068-86a684a51d53/GCF_014647875.1_ASM1464787v1_genomic.fna.gz --refList GCF_014647875.1_ASM1464787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647875.1_ASM1464787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:23:58,456] [INFO] Task succeeded: fastANI
[2024-01-24 15:23:58,490] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:23:58,490] [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_014647875.1	s__Streptomyces brasiliensis	100.0	3427	3439	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_003688995.1	s__Streptomyces shenzhenensis	86.4393	1939	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	86.1839	1931	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_001513965.1	s__Streptomyces cellostaticus	86.0826	1866	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827595.1	s__Streptomyces sp007827595	85.8034	1963	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650035.1	s__Streptomyces lucensis	85.497	1678	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	85.4772	1979	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	85.3944	1808	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	85.3545	1810	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	85.3116	1790	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004124325.1	s__Streptomyces sp004124325	85.2981	1729	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	85.1349	1828	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_000720835.1	s__Streptomyces achromogenes	85.129	1638	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	85.0622	1836	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	85.047	1832	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651035.1	s__Streptomyces lomondensis	85.0331	1732	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715395.1	s__Streptomyces sp006715395	85.0193	1831	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_014596915.1	s__Streptomyces sp014596915	84.9982	1717	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	84.9381	1738	3439	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	84.8818	1815	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	84.8579	1750	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	84.8488	1710	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.8127	1856	3439	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	84.7141	1612	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_000373625.1	s__Streptomyces sp000373625	84.5612	1556	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	84.4839	1735	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016482685.1	s__Streptomyces sp016482685	84.3864	1508	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090105.1	s__Streptomyces sp019090105	84.3853	1494	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704995.1	s__Streptomyces nodosus	83.3994	1589	3439	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	97.72	0.96	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:23:58,492] [INFO] GTDB search result was written to GCF_014647875.1_ASM1464787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:23:58,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:23:58,497] [INFO] DFAST_QC result json was written to GCF_014647875.1_ASM1464787v1_genomic.fna/dqc_result.json
[2024-01-24 15:23:58,497] [INFO] DFAST_QC completed!
[2024-01-24 15:23:58,498] [INFO] Total running time: 0h5m8s