[2024-01-24 13:46:55,091] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:55,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:55,093] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference
[2024-01-24 13:46:56,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:56,288] [INFO] Task started: Prodigal
[2024-01-24 13:46:56,288] [INFO] Running command: gunzip -c /var/lib/cwl/stge6a8f903-5c35-48aa-b5e2-f43f2859231b/GCF_014649375.1_ASM1464937v1_genomic.fna.gz | prodigal -d GCF_014649375.1_ASM1464937v1_genomic.fna/cds.fna -a GCF_014649375.1_ASM1464937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:26,258] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:26,258] [INFO] Task started: HMMsearch
[2024-01-24 13:47:26,259] [INFO] Running command: hmmsearch --tblout GCF_014649375.1_ASM1464937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference/reference_markers.hmm GCF_014649375.1_ASM1464937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:26,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:26,662] [INFO] Found 6/6 markers.
[2024-01-24 13:47:26,747] [INFO] Query marker FASTA was written to GCF_014649375.1_ASM1464937v1_genomic.fna/markers.fasta
[2024-01-24 13:47:26,747] [INFO] Task started: Blastn
[2024-01-24 13:47:26,747] [INFO] Running command: blastn -query GCF_014649375.1_ASM1464937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference/reference_markers.fasta -out GCF_014649375.1_ASM1464937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:28,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:28,037] [INFO] Selected 33 target genomes.
[2024-01-24 13:47:28,038] [INFO] Target genome list was writen to GCF_014649375.1_ASM1464937v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:28,131] [INFO] Task started: fastANI
[2024-01-24 13:47:28,131] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a8f903-5c35-48aa-b5e2-f43f2859231b/GCF_014649375.1_ASM1464937v1_genomic.fna.gz --refList GCF_014649375.1_ASM1464937v1_genomic.fna/target_genomes.txt --output GCF_014649375.1_ASM1464937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:35,783] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:35,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:35,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:35,810] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:48:35,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:48:35,810] [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 phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	87.1968	2214	3497	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	86.8865	2260	3497	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.8061	1850	3497	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	86.5479	2019	3497	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	86.5099	2072	3497	95	below_threshold
Streptomyces resistomycificus	strain=NRRL 2290	GCA_001270505.1	67356	67356	type	True	86.1644	2080	3497	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	86.1429	2122	3497	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.1319	2128	3497	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	86.0937	2117	3497	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.694	2167	3497	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.5888	2109	3497	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.3699	1847	3497	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.3621	1909	3497	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.2632	1542	3497	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.1422	1837	3497	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.0747	1820	3497	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	85.0002	1738	3497	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	84.8725	1560	3497	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	84.8642	1888	3497	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.8542	1507	3497	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	84.8255	1905	3497	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	84.8023	1764	3497	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	84.7299	1821	3497	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	84.7234	1796	3497	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.7043	1739	3497	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.6381	1822	3497	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.6234	1826	3497	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	84.5101	1852	3497	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	80.9802	1108	3497	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.0767	996	3497	95	below_threshold
Nocardia cyriacigeorgica	strain=DSM 44484	GCA_005863225.1	135487	135487	type	True	75.8569	412	3497	95	below_threshold
Nocardia cyriacigeorgica	strain=NBRC 100375	GCA_000308555.1	135487	135487	type	True	75.8142	421	3497	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	75.6089	587	3497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:35,812] [INFO] DFAST Taxonomy check result was written to GCF_014649375.1_ASM1464937v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:35,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:35,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:35,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference/checkm_data
[2024-01-24 13:48:35,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:35,910] [INFO] Task started: CheckM
[2024-01-24 13:48:35,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649375.1_ASM1464937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649375.1_ASM1464937v1_genomic.fna/checkm_input GCF_014649375.1_ASM1464937v1_genomic.fna/checkm_result
[2024-01-24 13:51:11,466] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:11,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:11,496] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:11,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:11,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649375.1_ASM1464937v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:11,498] [INFO] Task started: Blastn
[2024-01-24 13:51:11,498] [INFO] Running command: blastn -query GCF_014649375.1_ASM1464937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d02edb-c787-4d53-abb7-ae1298a2b489/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649375.1_ASM1464937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:13,627] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:13,632] [INFO] Selected 26 target genomes.
[2024-01-24 13:51:13,632] [INFO] Target genome list was writen to GCF_014649375.1_ASM1464937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:13,773] [INFO] Task started: fastANI
[2024-01-24 13:51:13,773] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a8f903-5c35-48aa-b5e2-f43f2859231b/GCF_014649375.1_ASM1464937v1_genomic.fna.gz --refList GCF_014649375.1_ASM1464937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649375.1_ASM1464937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:15,560] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:15,585] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:15,585] [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_014649375.1	s__Streptomyces aurantiogriseus	100.0	3492	3497	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_001896135.2	s__Streptomyces phaeoluteigriseus	88.0811	2083	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217285.1	s__Streptomyces sp004217285	87.9079	1708	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154575.1	s__Streptomyces bobili	87.8894	1714	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.61	97.61	0.88	0.85	3	-
GCF_013085465.1	s__Streptomyces cacaoi_A	87.4748	2279	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648915.1	s__Streptomyces phaeofaciens	87.2419	2207	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514205.1	s__Streptomyces griseoruber	86.9025	2257	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363835.1	s__Streptomyces sp004363835	86.8314	2242	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514285.1	s__Streptomyces sp001514285	86.5362	2075	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720255.1	s__Streptomyces griseus_I	86.3851	2145	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428885.1	s__Streptomyces sp001428885	86.2095	2027	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	86.1749	2222	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514265.1	s__Streptomyces resistomycificus	86.1301	2125	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	85.9449	2187	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685355.1	s__Streptomyces lincolnensis	85.8194	2145	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.95	3	-
GCA_000696115.1	s__Streptomyces olindensis	85.8132	2054	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	85.7677	1938	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346005.1	s__Streptomyces sp004346005	85.472	1972	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011193355.1	s__Streptomyces sp011193355	85.4607	1796	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343515.1	s__Streptomyces sp004343515	85.2773	2085	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_013046785.1	s__Streptomyces sp013046785	84.8354	1744	3497	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	84.6346	1824	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548275.1	s__Streptomyces sp010548275	84.3307	1896	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100315.1	s__Streptomyces indicus	81.6297	1491	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107395.1	s__Streptomyces fildesensis	79.6405	1307	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	98.63	0.90	0.87	4	-
GCF_002797655.1	s__Streptomyces sp002797655	79.0401	1310	3497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:15,587] [INFO] GTDB search result was written to GCF_014649375.1_ASM1464937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:15,588] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:15,593] [INFO] DFAST_QC result json was written to GCF_014649375.1_ASM1464937v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:15,593] [INFO] DFAST_QC completed!
[2024-01-24 13:52:15,593] [INFO] Total running time: 0h5m21s